Mercurial > repos > jjohnson > peptideshaker

annotate fasta_cli.xml @ 0:8b99cb00e1c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
author jjohnson
date Tue, 15 May 2018 14:50:35 -0400
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children fa76abf69433
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8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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1 <tool id="fasta_cli" name="FastaCLI" version="1.0">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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2 <description>
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3 Appends decoy sequences to FASTA files
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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4 </description>
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5 <macros>
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6 <import>macros_basic.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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10 <requirement type="package" version="3.0">zip</requirement>
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11 </requirements>
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12 <expand macro="stdio" />
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13 <command>
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14 <![CDATA[
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15
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16 ## #set $temp_stderr = "searchgui_stderr"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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17 #set $bin_dir = "bin"
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18
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19 mkdir output;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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20 cwd=`pwd`;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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21 export HOME=\$cwd;
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22
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23 ## echo the search engines to run
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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24 ##echo "$search_engines_options.engines";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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25 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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26
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27 cp "${input_database}" input_database.fasta;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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28
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29 ###########################################
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30 #### Creating decoy database ####
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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31 ###########################################
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32
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33 echo "Creating decoy database.";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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34 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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35 rm input_database.fasta;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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36 echo "Decoy database:";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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37 echo "\$cwd/input_database_concatenated_target_decoy.fasta";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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38
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39 exit_code_for_galaxy=\$?;
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40 ## cat $temp_stderr 2>&1;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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41 (exit \$exit_code_for_galaxy)
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42 ]]>
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43 </command>
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44 <inputs>
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45 <param format="fasta" name="input_database" type="data" label="Protein Database"
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46 help="Select FASTA database from history"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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47 </inputs>
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48 <outputs>
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49 <data name="input_database_concatenated_target_decoy" format="fasta" from_work_dir="input_database_concatenated_target_decoy.fasta" label="${tool.name}: FASTA file with decoys on ${on_string}" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
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54 <output name="input_database_concatenated_target_decoy" file="searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 Appends decoy sequences to FASTA files.
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61 </help>
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62 <expand macro="citations" />
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63 </tool>