Mercurial > repos > proteore > proteore_find_pathways

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author proteore
date Thu, 23 Aug 2018 08:33:45 -0400
parents 4da8523282cf
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1 <tool id="find_pathways" name="find pathways (keggrest)" version="2018.08.22">
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2 <requirements>
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3 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 Rscript $__tool_directory__/keggrest.R
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7
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8 #if $input.ids == "text"
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9 --id_list="$input.txt"
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10 #else
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11 --input="$input.file"
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12 --id_column="$input.ncol"
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13 --header="$input.header"
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14 #end if
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15
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16 --id_type="$ref_ids.id_type"
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17 --output="$output1"
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18 --nb_pathways="$nb_pathways"
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19 --ref="$ref_ids.ref_file"
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20
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21 ]]></command>
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22 <inputs>
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23 <conditional name="input" >
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24 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
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25 <option value="text">Copy/paste your identifiers</option>
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26 <option value="file" selected="true">Input file containing your identifiers</option>
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27 </param>
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28 <when value="text" >
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29 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
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30 <sanitizer invalid_char=''>
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31 <valid initial="string.printable">
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32 <remove value="&apos;"/>
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33 </valid>
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34 <mapping initial="none">
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35 <add source="&apos;" target="__sq__"/>
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36 </mapping>
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37 </sanitizer>
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38 </param>
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39 </when>
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40 <when value="file" >
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41 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
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42 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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43 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
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44 </when>
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45 </conditional>
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46 <conditional name="ref_ids">
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47 <param name="id_type" type="select" label="select your identifiers type :">
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48 <option value="uniprot">Uniprot Accession number</option>
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49 <option value="geneID">Entrez gene ID</option>
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50 </param>
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51 <when value="uniprot">
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52 <param name="ref_file" type="select" label="Select species" >
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53 <options from_data_table="uniprot_kegg_list"/>
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54 <option>Human</option>
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55 <option>Mouse</option>
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56 </param>
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57 </when>
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58 <when value="geneID">
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59 <param name="ref_file" type="select" label="Select species" >
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60 <options from_data_table="entrez_kegg_list"/>
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61 <option>Human</option>
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62 <option>Mouse</option>
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63 </param>
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64 </when>
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65 </conditional>
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66 <param type="integer" name="nb_pathways" label="Set the number of pathways to keep in result" value="10" help="pathways are sorted by percent of mapping gene by pathway in descending order"/>
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67 </inputs>
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68 <outputs>
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69 <data name="output1" format="tsv" />
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70 </outputs>
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71 <help><![CDATA[
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72 Pathview R script
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73 Arguments:
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74 --help Print this test
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75 --input tab file
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76 --id_list id list ',' separated
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77 --id_type type of input ids (uniprot_AC or geneID)
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78 --id_column number og column containg ids of interest
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79 --org organism : Hs , Mm, ...
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80 --nb_pathways number of pathways to return
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81 --header boolean
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82 --output output path
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83 --ref ref file (l.hsa.gene.RData, l.hsa.up.RData)
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84
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85 Example:
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86 Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE
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87
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88 ]]></help>
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89 <citations>
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90 <citation type="bibtex">
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91 @misc{githubKEGGREST,
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92 author = {LastTODO, FirstTODO},
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93 year = {TODO},
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94 title = {KEGGREST},
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95 publisher = {GitHub},
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96 journal = {GitHub repository},
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97 url = {https://github.com/Bioconductor/KEGGREST},
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98 }</citation>
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99 </citations>
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100 </tool>