Mercurial > repos > tduigou > rptools_rpranker

annotate rpranker.xml @ 4:1593c526737a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 387d0dd233c1d9948152a2d4af9e69ad10fe1b6a
author tduigou
date Thu, 23 Nov 2023 14:27:22 +0000
parents f9f7670fd5a6
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1 <tool id="rptools_rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Rank heterologous pathways according to their global score</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <regex match="WARNING" level="warning" />
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9 <regex match="ERROR" level="fatal" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #for $file in $pathway_collection
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13 ln -s '$file' '$file.element_identifier' &&
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14 #end for
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16 python -m rptools.rprank
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17 --pathways
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19 #for $file in $pathway_collection
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20 '$file.element_identifier'
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21 #end for
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23 > '$sorted_pathways'
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24 ]]></command>
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25 <inputs>
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26 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
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27 </inputs>
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28 <outputs>
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29 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <!-- test 1: check if identical outputs are produced with default parameters -->
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34 <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml"/>
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35 <output name="sorted_pathways" file="ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 Rank Pathways
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40 ================
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41
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42 Sort a list of pathways according to their global score.
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44 Input
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45 -----
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47 Required:
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49 * **Pathways**\ : List of pathway files (rpSBML)
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51 Output
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52 ------
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53
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54 * **Ranked Pathways**\ : Sorted names and scores of pathways
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55 ]]></help>
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56 <expand macro="creator"/>
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57 <citations>
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58 <citation type="doi">10.1038/s41467-022-32661-x</citation>
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59 </citations>
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60 </tool>