Mercurial > repos > galaxyp > peptideshaker
annotate peptide_shaker.xml @ 17:2f8e9d0351a8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
author | galaxyp |
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date | Fri, 10 Jun 2016 09:57:31 -0400 |
parents | c353378140ca |
children | ffed32e397cb |
rev | line source |
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17
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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2 <description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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3 Perform protein identification using various search engines based on results from SearchGUI |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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4 </description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty
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5 <macros> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty
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6 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty
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7 </macros> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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8 <requirements> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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9 <requirement type="package" version="1.11">peptide_shaker</requirement> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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10 </requirements> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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11 <expand macro="stdio" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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12 <command> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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13 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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14 #from datetime import datetime |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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17 #set $temp_stderr = "peptideshaker_stderr" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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18 |
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d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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19 |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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20 mkdir output_reports; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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21 cwd=`pwd`; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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22 |
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d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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23 cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin; |
d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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24 tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`; |
d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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25 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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26 ln -s '$searchgui_input' searchgui_input.zip && |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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27 ###################### |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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28 ## PeptideShakerCLI ## |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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29 ###################### |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
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30 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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31 -temp_folder \$cwd/PeptideShakerCLI |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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32 -experiment '$exp_str' |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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33 -sample '$samp_str' |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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34 -replicate 1 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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35 -identification_files \$cwd/searchgui_input.zip |
15 | 36 -out \$cwd/peptideshaker_output.cpsx |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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37 -zip \$cwd/peptideshaker_output.zip |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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38 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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39 -threads "\${GALAXY_SLOTS:-12}" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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40 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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41 ##Optional gene annotation parameter |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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42 #if $species_type.species_type_selector != 'no_species_type': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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43 -species_type "${species_type.species_type_selector}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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44 -species "${species_type.species}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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45 -species_update 1 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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46 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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47 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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48 ##Optional processing parameters: |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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49 #if $processing_options.processing_options_selector == "yes" |
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50 -protein_fdr "${processing_options.protein_fdr}" |
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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51 -peptide_fdr "${processing_options.peptide_fdr}" |
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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52 -psm_fdr "${processing_options.psm_fdr}" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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53 -ptm_score "${processing_options.ptm_score.ptm_score_selector}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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54 #if $processing_options.ptm_score.ptm_score_selector == 1 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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55 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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56 #if str($processing_options.ptm_score.ptm_threshold) != '' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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58 #end if |
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59 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" |
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61 -ptm_alignment "${processing_options.ptm_alignment}" |
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62 #end if |
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63 |
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64 ##Optional filtering parameters: |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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65 #if $filtering_options.filtering_options_selector == "yes": |
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66 -import_peptide_length_min "${filtering_options.min_peptide_length}" |
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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67 -import_peptide_length_max "${filtering_options.max_peptide_length}" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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68 -import_precurosor_mz "${filtering_options.max_precursor_error}" |
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
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69 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}" |
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70 ##-max_xtandem_e "${filtering_options.max_xtandem_e}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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71 ##-max_omssa_e "${filtering_options.max_omssa_e}" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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72 ##-max_mascot_e "${filtering_options.max_mascot_e}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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73 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
74 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
75 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
76 2>> $temp_stderr) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
77 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
78 && |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
79 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
80 echo "Running Reports"; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
81 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
82 ################################## |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
83 ## PeptideShaker Report options ## |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
84 ################################## |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
85 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
86 #if 'mzidentML' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
87 echo "Generating mzIdentML"; |
12
d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
iracooke
parents:
10
diff
changeset
|
88 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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89 -in \$cwd/peptideshaker_output.zip |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
90 -output_file output.mzid |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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91 -contact_first_name "Proteomics" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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92 -contact_last_name "Galaxy" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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93 -contact_email "galaxyp@umn.edu" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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94 -contact_address "galaxyp@umn.edu" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
95 -organization_name "University of Minnesota" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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96 -organization_email "galaxyp@umn.edu" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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97 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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98 2>> $temp_stderr) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
99 && |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
100 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
101 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
102 ## Generate Reports if the user has selected one of the 8 additional reports |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
103 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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104 ## and will not be passed to the command line |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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|
105 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
106 |
12
d298e0b6fd72
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
iracooke
parents:
10
diff
changeset
|
107 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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108 -temp_folder \$cwd/ReportCLI |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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109 -in \$cwd/peptideshaker_output.zip |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
110 -out_reports \$cwd/output_reports |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
111 #set $cleaned_list = str($outputs).split(',') |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
112 #if 'cps' in $cleaned_list: |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
113 #silent $cleaned_list.remove('cps') |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
|
114 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
115 #if 'mzidentML' in $cleaned_list: |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
116 #silent $cleaned_list.remove('mzidentML') |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
117 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
118 #if 'zip' in $cleaned_list: |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
119 #silent $cleaned_list.remove('zip') |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
120 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
121 ## Only numbers are left over. These corresponds to different reports. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
122 -reports #echo ','.join($cleaned_list)# |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
123 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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124 2>> $temp_stderr) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
125 && |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
126 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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127 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
128 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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129 #if '0' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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130 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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131 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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132 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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133 #if '1' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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134 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
135 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
136 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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137 #if '2' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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138 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
139 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
140 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
141 #if '3' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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142 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
143 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
144 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
145 #if '4' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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|
146 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
147 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
148 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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149 #if '5' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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150 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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changeset
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151 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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152 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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153 #if '6' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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154 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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155 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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156 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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157 #if '7' in str($outputs).split(','): |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff
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158 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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159 ; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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160 #end if |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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161 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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162 exit_code_for_galaxy=\$?; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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163 cat $temp_stderr 2>&1; |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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164 (exit \$exit_code_for_galaxy) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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165 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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166 ]]> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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167 </command> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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168 <inputs> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
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diff
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169 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" |
13 | 170 help="SearchGUI Results from History"> |
171 <options options_filter_attribute="metadata.searchgui_major_version" > | |
172 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> | |
173 </options> | |
174 </param> | |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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175 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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176 <conditional name="species_type"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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177 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
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178 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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179 <option value="Fungi">Fungi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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180 <option value="Plants">Plants</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
181 <option value="Metazoa">Metazoa</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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182 <option value="Vertebrates">Vertebrates</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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183 <option value="Protists">Protists</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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184 <option value="no_species_type" selected="true">No species restriction</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
185 </param> |
13 | 186 <when value="no_species_type"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
187 <when value="Protists"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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188 <param name="species" type="select" label="The species to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
189 help=""> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
190 <option value="Albugo laibachii">Albugo laibachii</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
191 <option value="Bigelowiella natans">Bigelowiella natans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
192 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
193 <option value="Emiliania huxleyi">Emiliania huxleyi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
194 <option value="Entamoeba histolytica">Entamoeba histolytica</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
195 <option value="Giardia lamblia">Giardia lamblia</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
196 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
197 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
198 <option value="Leishmania major">Leishmania major</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
199 <option value="Paramecium tetraurelia">Paramecium tetraurelia</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
200 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
201 <option value="Phytophthora infestans">Phytophthora infestans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
202 <option value="Phytophthora kernoviae">Phytophthora kernoviae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
203 <option value="Phytophthora lateralis">Phytophthora lateralis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
204 <option value="Phytophthora parasitica">Phytophthora parasitica</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
205 <option value="Phytophthora ramorum">Phytophthora ramorum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
206 <option value="Phytophthora sojae">Phytophthora sojae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
207 <option value="Plasmodium berghei">Plasmodium berghei</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
208 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
209 <option value="Plasmodium falciparum">Plasmodium falciparum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
210 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
211 <option value="Plasmodium vivax">Plasmodium vivax</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
212 <option value="Pythium aphanidermatum">Pythium aphanidermatum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
213 <option value="Pythium arrhenomanes">Pythium arrhenomanes</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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214 <option value="Pythium irregulare">Pythium irregulare</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
215 <option value="Pythium iwayamai">Pythium iwayamai</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
216 <option value="Pythium ultimum">Pythium ultimum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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|
217 <option value="Pythium vexans">Pythium vexans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
218 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
219 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
220 <option value="Toxoplasma gondii">Toxoplasma gondii</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
221 <option value="Trypanosoma brucei">Trypanosoma brucei</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
222 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
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|
223 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
224 <when value="Plants"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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225 <param name="species" type="select" label="The species to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
226 help=""> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
227 <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
228 <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
229 <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
230 <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
231 <option value="Brassica oleracea">Brassica oleracea</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
232 <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
233 <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
234 <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
235 <option value="Glycine max (Soybean)">Glycine max (Soybean)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
236 <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
237 <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
238 <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
239 <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
240 <option value="Oryza brachyantha">Oryza brachyantha</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
241 <option value="Oryza glumaepatula">Oryza glumaepatula</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
242 <option value="Oryza meridionalis">Oryza meridionalis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
243 <option value="Oryza nivara">Oryza nivara</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
244 <option value="Oryza punctata">Oryza punctata</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
245 <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
246 <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
247 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
248 <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
249 <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
250 <option value="Physcomitrella patens">Physcomitrella patens</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
251 <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
252 <option value="Populus trichocarpa">Populus trichocarpa</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
253 <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
254 <option value="Prunus persica (Peach)">Prunus persica (Peach)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
255 <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
256 <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
257 <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
258 <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
259 <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
260 <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
261 <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
262 <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
263 <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
264 <option value="Zea mays (Maize)">Zea mays (Maize)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
265 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
266 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
267 <when value="Metazoa"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
268 <param name="species" type="select" label="The species to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
269 help=""> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
270 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
271 <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
272 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
273 <option value="Anopheles darlingi">Anopheles darlingi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
274 <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
275 <option value="Apis mellifera ">Apis mellifera </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
276 <option value="Atta cephalotes ">Atta cephalotes </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
277 <option value="Bombyx mori ">Bombyx mori </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
278 <option value="Brugia malayi ">Brugia malayi </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
279 <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
280 <option value="Caenorhabditis briggsae ">Caenorhabditis briggsae </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
281 <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
282 <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
283 <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
284 <option value="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
285 <option value="Danaus plexippus ">Danaus plexippus </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
286 <option value="Daphnia pulex ">Daphnia pulex </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
287 <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
288 <option value="Drosophila ananassae ">Drosophila ananassae </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
289 <option value="Drosophila erecta ">Drosophila erecta </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
290 <option value="Drosophila grimshawi ">Drosophila grimshawi </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
291 <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
292 <option value="Drosophila mojavensis ">Drosophila mojavensis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
293 <option value="Drosophila persimilis ">Drosophila persimilis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
294 <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
295 <option value="Drosophila sechellia ">Drosophila sechellia </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
296 <option value="Drosophila simulans ">Drosophila simulans </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
297 <option value="Drosophila virilis ">Drosophila virilis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
298 <option value="Drosophila willistoni ">Drosophila willistoni </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
299 <option value="Drosophila yakuba ">Drosophila yakuba </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
300 <option value="Heliconius melpomene ">Heliconius melpomene </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
301 <option value="Helobdella robusta">Helobdella robusta</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
302 <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
303 <option value="Loa loa ">Loa loa </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
304 <option value="Lottia gigantea">Lottia gigantea</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
305 <option value="Megaselia scalaris ">Megaselia scalaris </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
306 <option value="Melitaea cinxia">Melitaea cinxia</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
307 <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
308 <option value="Nasonia vitripennis ">Nasonia vitripennis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
309 <option value="Nematostella vectensis ">Nematostella vectensis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
310 <option value="Onchocerca volvulus">Onchocerca volvulus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
311 <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
312 <option value="Pristionchus pacificus ">Pristionchus pacificus </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
313 <option value="Rhodnius prolixus">Rhodnius prolixus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
314 <option value="Schistosoma mansoni ">Schistosoma mansoni </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
315 <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
316 <option value="Strigamia maritima ">Strigamia maritima </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
317 <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
318 <option value="Tetranychus urticae">Tetranychus urticae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
319 <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
320 <option value="Trichinella spiralis ">Trichinella spiralis </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
321 <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
322 <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
323 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
324 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
325 <when value="Fungi"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
326 <param name="species" type="select" label="The species to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
327 help=""> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
328 <option value="Ashbya gossypii">Ashbya gossypii</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
329 <option value="Aspergillus clavatus">Aspergillus clavatus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
330 <option value="Aspergillus flavus">Aspergillus flavus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
331 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
332 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
333 <option value="Aspergillus nidulans">Aspergillus nidulans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
334 <option value="Aspergillus niger">Aspergillus niger</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
335 <option value="Aspergillus oryzae">Aspergillus oryzae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
336 <option value="Aspergillus terreus">Aspergillus terreus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
337 <option value="Blumeria graminis">Blumeria graminis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
338 <option value="Botrytis cinerea">Botrytis cinerea</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
339 <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
340 <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
341 <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
342 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
343 <option value="Dothistroma septosporum">Dothistroma septosporum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
344 <option value="Fusarium fujikuroi">Fusarium fujikuroi</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
345 <option value="Fusarium graminearum">Fusarium graminearum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
346 <option value="Fusarium oxysporum">Fusarium oxysporum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
347 <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
348 <option value="Fusarium solani">Fusarium solani</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
349 <option value="Fusarium verticillioides">Fusarium verticillioides</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
350 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
351 <option value="Colletotrichum graminicola">Colletotrichum graminicola</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
352 <option value="Komagataella pastoris">Komagataella pastoris</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
353 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
354 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
355 <option value="Magnaporthe poae">Magnaporthe poae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
356 <option value="Melampsora larici-populina">Melampsora larici-populina</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
357 <option value="Neosartorya fischeri">Neosartorya fischeri</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
358 <option value="Neurospora crassa">Neurospora crassa</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
359 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
360 <option value="Puccinia graminis">Puccinia graminis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
361 <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
362 <option value="Puccinia triticina">Puccinia triticina</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
363 <option value="Pyrenophora teres">Pyrenophora teres</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
364 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
365 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
366 <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
367 <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
368 <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
369 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
370 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
371 <option value="Sporisorium reilianum">Sporisorium reilianum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
372 <option value="Trichoderma reesei">Trichoderma reesei</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
373 <option value="Trichoderma virens">Trichoderma virens</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
374 <option value="Tuber melanosporum">Tuber melanosporum</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
375 <option value="Ustilago maydis">Ustilago maydis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
376 <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
377 <option value="Verticillium dahliae">Verticillium dahliae</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
378 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
379 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
380 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
381 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
382 <when value="Vertebrates"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
383 <param name="species" type="select" label="The species to use for the gene annotation" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
384 help=""> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
385 <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
386 <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
387 <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
388 <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
389 <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
390 <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
391 <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
392 <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
393 <option value="Cat (Felis catus)">Cat (Felis catus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
394 <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
395 <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
396 <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
397 <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
398 <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
399 <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
400 <option value="Cow (Bos taurus)">Cow (Bos taurus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
401 <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
402 <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
403 <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
404 <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
405 <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
406 <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
407 <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
408 <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
409 <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
410 <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
411 <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
412 <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
413 <option value="Horse (Equus caballus)">Horse (Equus caballus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
414 <option value="Human (Homo sapiens)">Human (Homo sapiens)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
415 <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
416 <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
417 <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
418 <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
419 <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
420 <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
421 <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
422 <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
423 <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
424 <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
425 <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
426 <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
427 <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
428 <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
429 <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
430 <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
431 <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
432 <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
433 <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
434 <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
435 <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
436 <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
437 <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
438 <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
439 <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
440 <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
441 <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
442 <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
443 <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
444 <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
445 <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
446 <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
447 <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
448 <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
449 <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
450 <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
451 <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
452 <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
453 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
454 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
455 </conditional> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
456 <conditional name="processing_options"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
457 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
458 <option value="no" selected="True">Default Processing Options</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
459 <option value="yes">Advanced Processing Options</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
460 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
461 <when value="no" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
462 <when value="yes"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
463 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
464 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
465 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
466 <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
467 help="default 95%: '95.0'" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
468 <conditional name="ptm_score"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
469 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
470 <option value="0" selected="True">A-score</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
471 <option value="1">PhosphoRS</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
472 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
473 <when value="0" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
474 <when value="1"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
475 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> |
16
c353378140ca
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty
galaxyp
parents:
15
diff
changeset
|
476 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
477 help="Automatic mode will be used if not set" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
478 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
479 </conditional> |
17
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents:
16
diff
changeset
|
480 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
481 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
482 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
483 </conditional> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
484 <conditional name="filtering_options"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
485 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
486 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
487 <option value="no" selected="True">Default Filtering Options</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
488 <option value="yes">Advanced Filtering Options</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
489 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
490 <when value="no" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
491 <when value="yes"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
492 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
493 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
494 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
495 help="Next option specifies units (Da or ppm)" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
496 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> |
17
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents:
16
diff
changeset
|
497 <option value="1">ppm</option> |
2f8e9d0351a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents:
16
diff
changeset
|
498 <option value="0">Daltons</option> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
499 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
500 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
501 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
502 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
503 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
504 </when> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
505 </conditional> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
506 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
507 <option value="zip">Zip File for import to Desktop App</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
508 <option value="mzidentML" selected="True">mzidentML File</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
509 <option value="3" >PSM Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
510 <option value="4" >Peptide Phosphorylation Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
511 <option value="5" >Peptide Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
512 <option value="6" >Protein Phosphorylation Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
513 <option value="7" >Protein Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
514 <option value="2">PSM Phosphorylation Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
515 <option value="0">Certificate of Analysis</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
516 <option value="1">Hierarchical Report</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
517 <option value="cps">CPS file</option> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
518 <validator type="no_options" message="Please select at least one output file" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
519 </param> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
520 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
521 </inputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
522 <outputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
523 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
524 <filter>'mzidentML' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
525 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
526 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
527 <filter>'cps' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
528 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
529 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
530 <filter>'zip' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
531 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
532 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
533 <filter>'0' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
534 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
535 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
536 <filter>'1' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
537 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
538 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
539 <filter>'2' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
540 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
541 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
542 <filter>'3' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
543 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
544 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
545 <filter>'4' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
546 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
547 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
548 <filter>'5' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
549 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
550 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
551 <filter>'6' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
552 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
553 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
554 <filter>'7' in outputs</filter> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
555 </data> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
556 </outputs> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
557 <tests> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
558 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
changeset
|
559 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
560 <param name="species_type_selector" value="no_species_type"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
561 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
562 <param name="filtering_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
563 <param name="outputs" value="zip,cps,3"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
564 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
565 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
566 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
567 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
568 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
changeset
|
569 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
570 <param name="species_type_selector" value="no_species_type"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
571 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
572 <param name="filtering_options_selector" value="yes"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
573 <param name="min_peptide_length" value="1"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
574 <param name="outputs" value="0,1,2,3,4,5,6,7"/> |
10
9d12b1d3c4ef
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9
iracooke
parents:
6
diff
changeset
|
575 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
576 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
577 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
578 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
579 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
580 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
581 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
582 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
583 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
584 <test> |
6
53bdfaed924d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents:
3
diff
changeset
|
585 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> |
0
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
586 <param name="species_type_selector" value="Vertebrates"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
587 <param name="species" value="Human (Homo sapiens)"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
588 <param name="processing_options_selector" value="no"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
589 <param name="filtering_options_selector" value="yes"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
590 <param name="min_peptide_length" value="1"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
591 <param name="outputs" value="5"/> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
592 <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
593 </test> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
594 </tests> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
595 <help> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
596 **What it does** |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
597 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
598 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
599 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
600 https://code.google.com/p/peptide-shaker/ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
601 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
602 https://code.google.com/p/searchgui/ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
603 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
604 ---- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
605 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
606 Reports |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
607 ======= |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
608 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
609 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
610 PSM Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
611 ---------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
612 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
613 * Protein(s): Protein(s) to which the peptide can be attached |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
614 * Sequence: Sequence of the peptide |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
615 * Variable Modifications: The variable modifications |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
616 * D-score: D-score for variable PTM localization |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
617 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
618 * Localization Confidence: The confidence in variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
619 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
620 * Spectrum File: The spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
621 * Spectrum Title: The title of the spectrum. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
622 * Spectrum Scan Number: The spectrum scan number. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
623 * RT: Retention time |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
624 * m/z: Measured m/z |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
625 * Measured Charge: The charge as given in the spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
626 * Identification Charge: The charge as inferred by the search engine. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
627 * Theoretical Mass: The theoretical mass of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
628 * Isotope Number: The isotope number targetted by the instrument. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
629 * Precursor m/z Error: The precursor m/z matching error. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
630 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
631 * Confidence: Confidence in percent associated to the retained PSM. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
632 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
633 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
634 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
635 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
636 Protein Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
637 -------------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
638 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
639 * Main Accession: Main accession of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
640 * Description: Description of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
641 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
642 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
643 * PI: Protein Inference status of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
644 * Secondary Accessions: Other accessions in the protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
645 * Protein Group: The complete protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
646 * #Peptides: Total number of peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
647 * #Validated Peptides: Number of validated peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
648 * #Unique: Total number of peptides unique to this protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
649 * #PSMs: Number of PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
650 * #Validated PSMs: Number of validated PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
651 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
652 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
653 * MW (kDa): Molecular Weight. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
654 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
655 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
656 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
657 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
658 * Score: Score of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
659 * Confidence: Confidence in percent associated to the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
660 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
661 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
662 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
663 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
664 Peptide Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
665 -------------- |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
666 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
667 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
668 * Protein(s): Protein(s) to which this peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
669 * AAs Before: The amino-acids before the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
670 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
671 * AAs After: The amino-acids after the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
672 * Modified Sequence: The peptide sequence annotated with variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
673 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
674 * Localization Confidence: The confidence in PTMs localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
675 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
676 * #Validated PSMs: Number of validated PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
677 * #PSMs: Number of PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
678 * Score: Score of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
679 * Confidence: Confidence in percent associated to the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
680 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
681 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
682 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
683 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
684 Hierachical Report |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
685 ------------------ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
686 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
687 * Main Accession: Main accession of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
688 * Description: Description of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
689 * PI: Protein Inference status of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
690 * Secondary Accessions: Other accessions in the protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
691 * Protein Group: The complete protein group (alphabetical order). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
692 * #Peptides: Total number of peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
693 * #Validated Peptides: Number of validated peptides. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
694 * #Unique: Total number of peptides unique to this protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
695 * #PSMs: Number of PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
696 * #Validated PSMs: Number of validated PSMs |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
697 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
698 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
699 * MW (kDa): Molecular Weight. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
700 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
701 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
702 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
703 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
704 * Score: Score of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
705 * Confidence: Confidence in percent associated to the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
706 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
707 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
708 * Protein(s): Protein(s) to which this peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
709 * AAs Before: The amino-acids before the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
710 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
711 * AAs After: The amino-acids after the sequence. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
712 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
713 * Localization Confidence: The confidence in PTMs localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
714 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
715 * #Validated PSMs: Number of validated PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
716 * #PSMs: Number of PSMs. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
717 * Score: Score of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff
changeset
|
718 * Confidence: Confidence in percent associated to the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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719 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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720 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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721 * Protein(s): Protein(s) to which the peptide can be attached. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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722 * Sequence: Sequence of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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723 * Modified Sequence: The peptide sequence annotated with variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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724 * Variable Modifications: The variable modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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725 * D-score: D-score for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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726 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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727 * Localization Confidence: The confidence in variable PTM localization. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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728 * Fixed Modifications: The fixed modifications. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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|
729 * Spectrum File: The spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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730 * Spectrum Title: The title of the spectrum. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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731 * Spectrum Scan Number: The spectrum scan number. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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732 * RT: Retention time |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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733 * m/z: Measured m/z |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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734 * Measured Charge: The charge as given in the spectrum file. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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735 * Identification Charge: The charge as inferred by the search engine. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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736 * Theoretical Mass: The theoretical mass of the peptide. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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737 * Isotope Number: The isotope number targetted by the instrument. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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738 * Precursor m/z Error: The precursor m/z matching error. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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739 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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740 * Confidence: Confidence in percent associated to the retained PSM. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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741 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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742 * Validation: Indicates the validation level of the protein group. |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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743 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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744 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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745 ------ |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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746 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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747 **Citation** |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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748 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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749 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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750 |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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751 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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752 </help> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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753 <expand macro="citations" /> |
a9e90cdcb97a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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754 </tool> |