Mercurial > repos > iuc > proteinortho_grab_proteins

annotate proteinortho_grab_proteins.xml @ 5:a87f7278b4ee draft

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planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791
author iuc
date Tue, 22 Nov 2022 16:51:10 +0000
parents 85ffb2cc6b64
children b183a90fe278
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85ffb2cc6b64 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 5627e0c3e34ba1357c276cb97e1ad077fe9b23c5"
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1 <tool id="proteinortho_grab_proteins" name="Proteinortho grab proteins" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
0
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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>
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4 <import>proteinortho_macros.xml</import>
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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"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
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10 #import re
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11 #for $f in $input_files#
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12 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
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13 #end for#
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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' &&
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16 #end if
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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
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19 --tofiles
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20 #if $regex:
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a87f7278b4ee planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791
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21 '$regex'
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22 #end if
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a87f7278b4ee planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791
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23 $source
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24 #if $query.querytype == "string":
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25 '$query.querystring'
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26 #else:
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27 ../query
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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28 #end if
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29 #for $f in $input_files#
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30 ../${re.sub('[^\w\-_.]', '_', f.element_identifier)}
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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31 #end for#
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32 ]]></command>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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33 <inputs>
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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34 <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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35 <conditional name="query">
d348c3a151d9 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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36 <param name="querytype" type="select" label="Query type">
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37 <option value="string" selected="true">String</option>
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38 <option value="file">orthology-groups output file</option>
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39 </param>
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40 <when value="string">
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41 <param name="querystring" type="text" label="A string of the protein/gene name/identifier that you want to search">
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a87f7278b4ee planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791
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42 <validator type="regex" negate="true" message="Identifier must not end with a backslash">.*\\$</validator>
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43 <sanitizer invalid_char="">
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44 <valid initial="string.letters,string.digits">
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45 <add value="!"/>
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46 <add value="="/>
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47 <add value="-"/>
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48 <add value="."/>
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49 <add value="*"/>
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50 <add value="?"/>
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51 <add value="+"/>
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52 <add value="\\"/>
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53 <add value="_"/>
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54 <add value="|"/>
1
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55 <add value="\t"/>
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56 <add value="&#9;"/> <!-- tab -->
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57 <add value=","/>
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58 <add value=";"/>
0
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59 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
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60 <add value="&#93;"/> <!-- right square bracket -->
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61 <add value="&#40;"/> <!-- left parenthesis -->
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62 <add value="&#41;"/> <!-- right parenthesis -->
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63 </valid>
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64 </sanitizer>
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65 </param>
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66 </when>
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67 <when value="file">
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68 <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."/>
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69 </when>
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70 </conditional>
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71 <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]"/>
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72 <param argument="--source" type="boolean" checked="false" truevalue="-source" falsevalue="" label="Add the filename to the gene/protein-name [--source]"/>
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73 </inputs>
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74 <outputs>
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75 <collection name="listproteinorthograbproteins" type="list" label="${tool.name} on ${on_string}: list of fasta">
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76 <discover_datasets pattern="__designation__" format="fasta" directory="output" visible="false"/>
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77 </collection>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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82 <param name="querytype" value="string"/>
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83 <param name="querystring" value="E_1"/>
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84 <output_collection name="listproteinorthograbproteins" count="1"/>
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85 </test>
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86 <test>
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87 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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88 <param name="querytype" value="string"/>
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89 <param name="regex" value="true"/>
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90 <param name="source" value="true"/>
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91 <param name="querystring" value="M..2"/>
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92 <output_collection name="listproteinorthograbproteins" count="1"/>
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93 </test>
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94 <test>
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95 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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96 <param name="querytype" value="file"/>
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97 <param name="queryfile" value="result.proteinortho.tsv"/>
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98 <output_collection name="listproteinorthograbproteins" count="34"/>
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99 </test>
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100 </tests>
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101 <help><![CDATA[proteinortho grab proteins
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102
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103 **What it does**
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104
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105 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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106
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107 **Other Proteinortho-Tools for downstream analysis**
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108
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109 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
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110
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111 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
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112 ]]>
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113 </help>
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114 <expand macro="citations"/>
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115 </tool>