Mercurial > repos > galaxyp > fragpipe
annotate fragpipe.xml @ 3:da9ebef968bd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15
author | galaxyp |
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date | Thu, 12 Sep 2024 08:06:44 +0000 |
parents | 14785481da2b |
children | e969a182e3cb |
rev | line source |
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14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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1 <tool id="fragpipe" name="FragPipe - Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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2 <description>Data analysis for mass spectrometry-based proteomics</description> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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3 <macros> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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4 <import>macros.xml</import> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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5 </macros> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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6 <expand macro="requirements"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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7 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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8 <stdio> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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9 <!-- The error code from individual tools run by FragPipe is not always propogated to the FragPipe process exit code --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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10 <regex match="exit code: [^0]" |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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11 source="stdout" |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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12 level="fatal" |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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13 description="A FragPipe pipeline process returned non-zero exit code."/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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14 </stdio> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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15 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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16 <version_command>fragpipe --help | grep 'FragPipe v'</version_command> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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17 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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18 <!-- |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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19 FragPipe wrapper command: |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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20 - Links input files |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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21 - Modifies database path in workflow file |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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22 - Runs Philosopher to add decoys and contaminants |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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23 - Runs FragPipe, passing paths to MSFragger, Philosopher, Python, and IonQuant |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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24 --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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25 <command detect_errors="exit_code"><![CDATA[ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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26 ## Create symlink for workflow output |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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27 ln -s $workflow_configfile fp.workflow; |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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28 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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29 ## The user may opt to only output the workflow to review the parameters. If they haven't selected this option, we prepare and run FragPipe. |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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30 #if not $workflow_only |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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31 @PREPARE_ENVIRONMENT@ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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32 @PREPARE_INPUTS@ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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33 @PREPARE_DATABASE@ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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34 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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35 ## Run FragPipe |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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36 '$__tool_directory__/fragpipe' |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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37 --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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38 --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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39 --headless |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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40 --threads \${GALAXY_SLOTS:-8} |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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41 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ] |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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42 --workflow fp.workflow --manifest fp.manifest |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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43 --workdir outputs |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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44 --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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45 --config-philosopher \$(which philosopher) |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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46 --config-python \$(which python) |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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47 --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar && |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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48 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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49 @PREPARE_OUTPUTS@ |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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50 #end if |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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51 ]]></command> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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52 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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53 <!-- Config file is a FragPipe workflow file --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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54 <configfiles> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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55 <expand macro="workflow_configfile" /> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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56 </configfiles> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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57 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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58 <inputs> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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59 <!-- License agreements --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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60 <expand macro="license_agreements"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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61 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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62 <!-- Input scan samples --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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63 <expand macro="samples"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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64 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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65 <!-- Searched database --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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66 <expand macro="fragger_database"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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67 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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68 <!-- Workflow input, if the user chooses to re-use existing FragPipe workflow. --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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69 <expand macro="workflow"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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70 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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71 <!-- Only generate a workflow, don't run FragPipe --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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72 <param name="workflow_only" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Only generate the workflow output"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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73 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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74 <param name="output_options" label="Additional outputs" type="select" multiple="true" display="checkboxes" optional="true"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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75 <option value="workflow">FragPipe Workflow</option> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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76 <option value="log">FragPipe Log</option> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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77 <option value="combined_outputs">FragPipe Combined Outputs</option> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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78 <option value="concatenated_outputs">TSV Outputs Concatenated</option> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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79 </param> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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80 </inputs> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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81 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
82 <outputs> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
83 <!-- Workflow file used by FragPipe --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
84 <data name="output_workflow" format="txt" label="${tool.name} on ${on_string}: workflow" from_work_dir="fp.workflow"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
85 <filter>workflow_only or (output_options and 'workflow' in output_options)</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
86 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
87 <!-- FragPipe log --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
88 <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="outputs/log_*.txt"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
89 <filter>not workflow_only and output_options and 'log' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
90 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
91 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
92 <!-- Collection outputs comprised of separate results for different experiments --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
93 <collection name="output_psm" type="list" label="${tool.name} - ${on_string}: psm.tsv" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
94 <filter>not workflow_only</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
95 <discover_datasets pattern="(?P<designation>.+\.psm.tsv)" ext="tabular" directory="outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
96 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
97 <collection name="output_ion" type="list" label="${tool.name} - ${on_string}: ion.tsv" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
98 <filter>not workflow_only</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
99 <discover_datasets pattern="(?P<designation>.+\.ion.tsv)" ext="tabular" directory="outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
100 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
101 <collection name="output_peptide" type="list" label="${tool.name} - ${on_string}: peptide.tsv" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
102 <filter>not workflow_only</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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103 <discover_datasets pattern="(?P<designation>.+\.peptide.tsv)" ext="tabular" directory="outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
104 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
105 <collection name="output_protein" type="list" label="${tool.name} - ${on_string}: protein.tsv" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
106 <filter>not workflow_only</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
107 <discover_datasets pattern="(?P<designation>.+\.protein.tsv)" ext="tabular" directory="outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
108 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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109 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
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110 <!-- Combined results from all experimental groups --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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111 <collection name="combined_outputs" type="list" label="${tool.name} - ${on_string}: Combined Outputs" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
112 <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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113 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
114 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
115 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
116 <!-- Galaxy-wrapper concatenated results --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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117 <data name="concat_psm_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
118 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
119 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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120 <data name="concat_ion_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
121 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
122 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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123 <data name="concat_peptide_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
124 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
125 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
126 <data name="concat_protein_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
127 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
128 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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129 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
130 <!-- PTM-Shepherd Results --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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131 <data name="global_profile_tsv" format="tabular" label="${tool.name} on ${on_string}: global.profile.tsv" from_work_dir="outputs/global.profile.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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132 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
133 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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134 <data name="global_summary_tsv" format="tabular" label="${tool.name} on ${on_string}: global.modsummary.tsv" from_work_dir="outputs/global.modsummary.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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135 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
136 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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137 <data name="global_diagmine_tsv" format="tabular" label="${tool.name} on ${on_string}: global.diagmine.tsv" from_work_dir="outputs/global.diagmine.tsv"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
138 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
139 </data> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
140 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
141 <!-- |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
142 TMT/iTRAW Results |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
143 Only produced by TMT, TRAQ, and SLC workflows |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
144 --> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
145 <collection name="tmt_results" type="list" label="${tool.name} - ${on_string}: TMT Results" > |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
146 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
147 <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
148 </collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
149 </outputs> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
150 |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
changeset
|
151 <tests> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
152 <test expect_num_outputs="11"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
153 <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff
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|
154 <param name="database_name" value="default/test.fasta" ftype="fasta"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
155 <param name="manifest" value="default/test.manifest" ftype="tabular"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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|
156 <param name="workflow_name" value="Default"/> |
3
da9ebef968bd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15
galaxyp
parents:
0
diff
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|
157 <param name="label_free_quantification_run" value="ionquant"/> |
0
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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158 <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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159 <param name="license_agreements" value="true"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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160 <output name="concat_psm_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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161 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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162 <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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163 <has_text text="sample1"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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164 </assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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165 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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166 <output name="concat_ion_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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167 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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168 <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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169 <has_text text="sample1"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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170 </assert_contents> |
14785481da2b
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171 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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172 <output name="concat_peptide_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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173 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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174 <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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175 <has_text text="sample1"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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176 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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177 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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178 <output name="concat_protein_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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179 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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180 <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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181 <has_text text="sample1"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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182 </assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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183 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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184 <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains"> |
14785481da2b
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185 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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186 <has_text text="crystalc.run-crystalc=false"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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187 </assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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188 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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189 <output name="log" ftype="txt"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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190 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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191 <has_text text="FragPipe version 20.0"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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192 </assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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193 </output> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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194 <output_collection name="combined_outputs" type="list"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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195 <element name="combined_protein.tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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196 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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197 <has_text text="Protein	Protein ID	Entry Name	Gene	Protein Length	Organism	Protein Existence	Description	Protein Probability	Top Peptide Probability	Combined Total Peptides	Combined Spectral Count	Combined Unique Spectral Count	Combined Total Spectral Count	sample1 Spectral Count	sample2 Spectral Count	sample1 Intensity	sample2 Intensity	Indistinguishable Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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198 </assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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199 </element> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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200 </output_collection> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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201 </test> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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202 <test expect_num_outputs="11"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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203 <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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204 <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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205 <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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206 <param name="annotation" value="tmt11/test.annotation" ftype="tabular"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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207 <param name="workflow_name" value="TMT11"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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208 <param name="output_options" value="workflow,log,concatenated_outputs"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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209 <param name="license_agreements" value="true"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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210 <output name="concat_psm_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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211 <assert_contents> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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212 <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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213 <has_text text="sample1"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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214 </assert_contents> |
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215 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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216 <output name="concat_ion_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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217 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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218 <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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219 <has_text text="sample1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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220 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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221 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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222 <output name="concat_peptide_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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223 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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224 <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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225 <has_text text="sample1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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226 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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227 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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228 <output name="concat_protein_tsv" ftype="tabular"> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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229 <assert_contents> |
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230 <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> |
14785481da2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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231 <has_text text="sample1"/> |
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232 </assert_contents> |
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233 </output> |
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234 <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"> |
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235 <assert_contents> |
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236 <has_text text="crystalc.run-crystalc=false"/> |
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237 </assert_contents> |
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238 </output> |
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239 <output name="log" ftype="txt"> |
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240 <assert_contents> |
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241 <has_text text="FragPipe version 20.0"/> |
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242 </assert_contents> |
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243 </output> |
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244 <output_collection name="tmt_results" type="list"> |
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245 <element name="abundance_gene_MD.tsv" ftype="tabular"> |
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246 <assert_contents> |
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247 <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> |
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248 </assert_contents> |
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249 </element> |
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250 <element name="ratio_gene_MD.tsv" ftype="tabular"> |
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251 <assert_contents> |
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252 <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> |
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253 </assert_contents> |
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254 </element> |
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255 </output_collection> |
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256 </test> |
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257 </tests> |
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258 |
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259 <help><![CDATA[ |
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260 **FragPipe** |
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261 |
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262 FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. |
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263 FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification. |
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264 |
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265 FragPipe_ runs a user selected analysis workflow_ |
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266 |
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267 **License Agreements** |
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268 |
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269 @LICENSE_AGREEMENTS@ |
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270 |
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271 .. _FragPipe: https://fragpipe.nesvilab.org |
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272 .. _MSFragger: https://msfragger.nesvilab.org |
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273 .. _workflow: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_workflows.html |
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274 |
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275 ]]></help> |
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276 <expand macro="citations" /> |
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277 </tool> |