Mercurial > repos > galaxyp > metaquantome_sample
annotate metaquantome_sample.xml @ 5:b2a41837a07e draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 12499da76192d2a61bfd475bc6e21dbe6f23643a"
author | galaxyp |
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date | Wed, 16 Jun 2021 19:56:05 +0000 |
parents | 5d323db9d454 |
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5d323db9d454
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
galaxyp
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1 <tool id="metaquantome_sample" name="metaQuantome: create samples file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
0
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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2 <description> by specifying the experiment's groups and associated column names</description> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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3 <macros> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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4 <import>macros.xml</import> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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5 </macros> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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6 <command detect_errors="exit_code"><![CDATA[ |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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7 #set $samp_header = 'group\tcolnames' |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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8 echo -e '${samp_header}' > samp_file.tab; |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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9 #if $samps_args.samps_src == 'build': |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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10 #for $s in $samps_args.samps |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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11 #set $sample = str($s.group_name) + '\t' + str($s.col_names) |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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12 echo -e '${sample}' >> samp_file.tab; |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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13 #end for |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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14 #else: |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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15 #for $s in $samps_args.samps |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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16 cat ${samps_args.file} | cut -f ${s.col_names} | |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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17 head -n 1 | tr '\t' ',' | |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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18 cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab; |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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19 #end for |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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20 #end if |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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21 ]]></command> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
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22 <inputs> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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23 <conditional name="samps_args"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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24 <param name="samps_src" type="select" label="Sample file creation method"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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25 <option value="build">Manually specify experimental conditions and samples</option> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
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26 <option value="history">Select samples from the header of an existing file</option> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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27 </param> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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changeset
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28 <when value="build"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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29 <repeat name="samps" title="Samples"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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30 <param name="group_name" type="text" label="Group name" help="Provide a name for the experimental condition."/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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31 <param name="col_names" type="text" label="Column" |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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32 help="Give a comma-separated list of the column names that correspond to samples within the experimental condition." /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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33 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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34 </when> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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35 <when value="history"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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36 <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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37 <repeat name="samps" title="Samples"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
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38 <param name="group_name" type="text" label="Group name" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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39 <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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40 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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41 </when> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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42 </conditional> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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43 </inputs> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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44 <outputs> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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45 <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name} ${on_string}" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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46 </outputs> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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47 <tests> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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48 <test> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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49 <param name="samps_src" value="build" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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50 <repeat name="samps"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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51 <param name="group_name" value="NS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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52 <param name="col_names" value="X737NS,X852NS,X867NS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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53 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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54 <repeat name="samps"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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55 <param name="group_name" value="WS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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56 <param name="col_names" value="X737WS,X852WS,X867WS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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57 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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58 <output name="samples_file" file="samples.tab" ftype="tabular"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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59 </test> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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60 <test> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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61 <param name="samps_src" value="history" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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62 <param name="file" value="int_737_test.tab" ftype="tabular" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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63 <repeat name="samps"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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64 <param name="group_name" value="NS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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65 <param name="col_names" value="3,5,7"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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66 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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67 <repeat name="samps"> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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68 <param name="group_name" value="WS"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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69 <param name="col_names" value="2,4,6"/> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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70 </repeat> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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71 <output name="samples_file" file="samples.tab" ftype="tabular" /> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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72 </test> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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73 </tests> |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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74 <help><![CDATA[ |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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75 metaQuantome: create samples file |
2bfd8e0a138d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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76 ================================= |
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77 |
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78 The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. An example file is shown below. |
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79 |
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80 *Create samples file* |
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81 ===== ==================== |
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82 group colnames |
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83 ===== ==================== |
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84 NS X737NS,X852NS,X867NS |
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85 WS X737WS,X852WS,X867WS |
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86 ===== ==================== |
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87 |
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88 |
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89 There are two methods for generating this input file: |
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90 |
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91 1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*). |
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92 |
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93 |
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94 2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 3, 5, and 7 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below. |
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95 |
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96 *int.tab file* |
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97 ============ ====== ====== ====== ====== ====== ====== |
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98 peptide X737WS X737NS X852WS X852NS X867WS X867NS |
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99 ============ ====== ====== ====== ====== ====== ====== |
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100 LPGQQHGTPSAK 1 2 3 4 5 6 |
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101 ELPGLAALTDK 7 8 9 10 11 12 |
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102 ============ ====== ====== ====== ====== ====== ====== |
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103 |
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104 |
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105 Questions, Comments, Problems, Kudos |
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106 ------------------------------------ |
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107 |
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108 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. |
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109 ]]></help> |
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110 <citations> |
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111 <citation type="doi">10.1093/bioinformatics/btv033</citation> |
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112 </citations> |
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113 </tool> |