Mercurial > repos > proteore > proteore_pathview_mapping
diff Pathview.xml @ 0:097bb3ed2b4d draft
planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
| author | proteore |
|---|---|
| date | Wed, 22 Aug 2018 11:30:23 -0400 |
| parents | |
| children | 059f17f98ab5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Pathview.xml Wed Aug 22 11:30:23 2018 -0400 @@ -0,0 +1,234 @@ +<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.22"> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/PathView.R + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + #if $species.pathways.pathways_id == "pathways_ids" + --pathways_id="$species.pathways.pids" + #else + --pathways_id="$species.pathways.pids" + #end if + --id_type="$id_type" + --native_kegg="$native" + + #if $input.ids=="file" + #if $input.expression_values.nb_exp =="1" + --expression_values1="$input.expression_values.e1" + #else if $input.expression_values.nb_exp =="2" + --expression_values1="$input.expression_values.e1" + --expression_values2="$input.expression_values.e2" + #else if $input.expression_values.nb_exp =="3" + --expression_values1="$input.expression_values.e1" + --expression_values2="$input.expression_values.e2" + --expression_values3="$input.expression_values.e3" + #end if + #end if + + --species=${species.ref_file} + + ]]></command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="text">Copy/paste your identifiers</option> + <option value="file" selected="true">Input file containing your identifiers</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <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' /> + <conditional name="expression_values"> + <param name="nb_exp" type="select" label="How many expression values column in your file ?"> + <option value="0" >0</option> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + </param> + <when value="0"> + </when> + <when value="1"> + <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/> + </when> + <when value="2"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + </when> + <when value="3"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + <param name="e3" type="text" value="" label="Third column number of your expression data"/> + </when> + </conditional> + </when> + </conditional> + <param name="id_type" type="select" label="select your identifiers type :"> + <option value="uniprotID">Uniprot Accession number</option> + <option value="geneID">Entrez gene ID</option> + </param> + + <conditional name="species"> + <param name="ref_file" type="select" label="Select species" > + <options from_data_table="kegg_pathways"/> + <option value="hsa"/> + <option value="mmu"/> + </param> + <when value="hsa"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway id(s)</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="hsa_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + </when> + <when value="mmu"> + <conditional name="pathways"> + <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> + <option value="pathways_names">KEGG pathway name(s)</option> + <option value="pathways_ids">KEGG pathway id(s)</option> + </param> + <when value="pathways_names"> + <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> + <options from_data_table="mmu_pathways"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="pathways_ids"> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + </when> + </conditional> + <param name="native" type="select" label="Choose the output graph format"> + <option value="true">KEGG graph (.png)</option> + <option value="false">Graphviz layout engine (.pdf)</option> + </param> + </inputs> + <outputs> + <data name="graphviz_from_file" format="pdf" label="KEGG mapping with ${input.file.name}"> + <filter>native=="false" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> + </data> + <data name="kegg_from_file" format="png" label="KEGG mapping with ${input.file.name}"> + <filter>native=="true" and input["ids"] == "file"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/> + </data> + <data name="graphviz_from_list" format="pdf" label="KEGG mapping with given ids"> + <filter>native=="false" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> + </data> + <data name="kegg_from_list" format="png" label="KEGG mapping with given ids"> + <filter>native=="true" and input["ids"] == "text"</filter> + <discover_datasets pattern="(?P<designation>.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/> + </data> + </outputs> + <tests> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_et_al_2017_OK.txt"/> + <param name="header" value="true"/> + <param name="ncol" value="c1"/> + </conditional> + <conditional name="pathways"> + <param name="pathways_id" value="pathways_ids"/> + <param name="pids" value="04514,05167,00010"/> + </conditional> + <param name="id_type" value="uniprotID"/> + <param name="species" value="hsa"/> + <param name="native" value="true"/> + <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/> + <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. + +Select an input file containing ids in a column, set header and column number or copy/paste your ids. + +Select your identifier type and a species of interest (for now only human available). + +Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) + +Select the graph format : KEGG or graphviz + +Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways. + +Output : One file (png or pdf) for each selected pathway. + +----- + +.. class:: infomark + +**Authors** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gkx372</citation> + <citation type="bibtex"> +@misc{renameTODO, + author = {Weijun Luo}, + year = {2013}, + title = {pathview}, + url = {https://bioconductor.org/packages/release/bioc/html/pathview.html}, +}</citation> + </citations> +</tool>