annotate proteinortho_grab_proteins.xml @ 1:fa2d1e652ec1 draft

"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
author iuc
date Tue, 14 Sep 2021 11:39:49 +0000
parents d348c3a151d9
children 85ffb2cc6b64
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1
fa2d1e652ec1 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
iuc
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1 <tool id="proteinortho_grab_proteins" name="Proteinortho grab proteins" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFLE@">
0
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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2 <description>finds genes/proteins in a given fasta file</description>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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3 <macros>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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4 <import>proteinortho_macros.xml</import>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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5 </macros>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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6 <expand macro="requirements"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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7 <expand macro="version_command"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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8 <command detect_errors="exit_code"><![CDATA[
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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9 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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10 #import re
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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11 #for $f in $input_files#
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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12 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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13 #end for#
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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14 #if $query.querytype == "file":
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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15 ln -sf '$query.queryfile' 'query' &&
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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16 #end if
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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17 mkdir output && cd output &&
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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18 proteinortho_grab_proteins.pl
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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19 --tofiles
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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20 #if $regex:
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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21 $regex
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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22 #end if
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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23 #if $source:
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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24 $source
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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25 #end if
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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26 #if $query.querytype == "string":
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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27 '$query.querystring'
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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28 #else:
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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29 ../query
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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30 #end if
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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31 #for $f in $input_files#
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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32 ../${re.sub('[^\w\-_.]', '_', f.element_identifier)}
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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33 #end for#
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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34 ]]></command>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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35 <inputs>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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36 <param name="input_files" type="data" format="fasta" multiple="true" min="1" label="Select the input fasta files"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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37 <conditional name="query">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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38 <param name="querytype" type="select" label="Query type">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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39 <option value="string" selected="true">String</option>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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40 <option value="file">orthology-groups output file</option>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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41 </param>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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42 <when value="string">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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43 <param name="querystring" type="text" label="A string of the protein/gene name/identifier that you want to search">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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44 <sanitizer invalid_char="">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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45 <valid initial="string.letters,string.digits">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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46 <add value="!"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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47 <add value="="/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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48 <add value="-"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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49 <add value="."/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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50 <add value="*"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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51 <add value="?"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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52 <add value="+"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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53 <add value="\\"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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54 <add value="_"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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55 <add value="|"/>
1
fa2d1e652ec1 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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56 <add value="\t"/>
fa2d1e652ec1 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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57 <add value="&#9;"/> <!-- tab -->
fa2d1e652ec1 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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58 <add value=","/>
fa2d1e652ec1 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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59 <add value=";"/>
0
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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60 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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61 <add value="&#93;"/> <!-- right square bracket -->
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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62 <add value="&#40;"/> <!-- left parenthesis -->
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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63 <add value="&#41;"/> <!-- right parenthesis -->
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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64 </valid>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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65 </sanitizer>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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66 </param>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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67 </when>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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68 <when value="file">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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69 <param name="queryfile" type="data" format="tabular" label="A orthology-groups file" help="For each group a fasta file is generated containing all proteins/genes of that group."/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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70 </when>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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71 </conditional>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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72 <param argument="--regex" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Enable regular expressions (perl)" help="If not: the string is escaped (e.g. | -> \|) [-E]"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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73 <param argument="--source" type="boolean" checked="false" truevalue="-source" falsevalue="" label="Add the filename to the gene/protein-name [--source]"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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74 </inputs>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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75 <outputs>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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76 <collection name="listproteinorthograbproteins" type="list" label="${tool.name} on ${on_string}: list of fasta">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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77 <discover_datasets pattern="__designation__" format="fasta" directory="output" visible="false"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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78 </collection>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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79 </outputs>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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80 <tests>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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81 <test>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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82 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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83 <param name="querytype" value="string"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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84 <param name="querystring" value="E_1"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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85 <output_collection name="listproteinorthograbproteins" count="1"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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86 </test>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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87 <test>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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88 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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89 <param name="querytype" value="string"/>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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90 <param name="regex" value="true"/>
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91 <param name="source" value="true"/>
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92 <param name="querystring" value="M..2"/>
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93 <output_collection name="listproteinorthograbproteins" count="1"/>
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94 </test>
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95 <test>
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96 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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97 <param name="querytype" value="file"/>
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98 <param name="queryfile" value="result.proteinortho.tsv"/>
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99 <output_collection name="listproteinorthograbproteins" count="34"/>
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100 </test>
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101 </tests>
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102 <help><![CDATA[proteinortho grab proteins
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103
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104 **What it does**
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105
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106 proteinortho_grab_proteins : find gene(s)/protein(s) in a given fasta file and retrieve their sequence(s). You can also use a orthology-groups file, then all sequences for each group (one line of the file) is outputted. This can result in many files!
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107
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108 **Other Proteinortho-Tools for downstream analysis**
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109
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110 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
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111
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112 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
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113 ]]>
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114 </help>
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115 <expand macro="citations"/>
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116 </tool>