Mercurial > repos > glogobyte > isoread
changeset 23:d2eea02053a0 draft
Deleted selected files
| author | glogobyte |
|---|---|
| date | Wed, 28 Oct 2020 08:13:30 +0000 |
| parents | d766563ab56d |
| children | d9b2a7df9d4b |
| files | toolExample_v2.xml |
| diffstat | 1 files changed, 0 insertions(+), 136 deletions(-) [+] |
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--- a/toolExample_v2.xml Thu Oct 22 08:25:23 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ - -<tool id="fa_gc_content_1" name="IsoRead: miR and isomiR identification and classification" version="0.1.0"> - <description>for each sequence in a file</description> - <requirements> - <requirement type="package" version="1.7">fpdf</requirement> - <requirement type="package" version="0.8">logomaker</requirement> - <requirement type="package" version="0.6.0">plotnine</requirement> - <requirement type="package" version="3.7.4">python</requirement> - <requirement type="package" version="1.17.3">numpy</requirement> - <requirement type="package" version="3.1.2">matplotlib</requirement> - <requirement type="package" version="0.9.0">seaborn</requirement> - <requirement type="package" version="1.0.3">pandas</requirement> - </requirements> - <command> - #set controls=[] - #for $input in $control# - $controls.extend([str($input.element_identifier),str($input)]) - #end for# - #set treateds=[] - #for $input in $treated# - $treateds.extend([str($input.element_identifier),str($input)]) - #end for# - #if $mir_input.database == "1": - #if $f.fil == "1": - #set path=$mir_input.genome1.fields.path - python -W ignore $__tool_directory__/mirbase_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2" - #end if - #if $f.fil == "2": - #set path=$mir_input.genome1.fields.path - python -W ignore $__tool_directory__/mirbase_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2" - #end if - #else: - #if $f.fil == "1": - #set path=$mir_input.genome2.fields.value - python -W ignore $__tool_directory__/mirgene_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2" - #end if - #if $f.fil == "2": - #set path=$mir_input.genome2.fields.value - python -W ignore $__tool_directory__/mirgene_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2" - #end if - #end if - - </command> - <inputs> - <param name="analysis" type="select" label="Discover miR with templated or/and non-templated isomiRs" help="Choose the category of miRNAs for detection"> - <option value="1" selected="true">Detection of only templated miRNAs</option> - <option value="2">Detection of templated and non-templated miRNAs</option> - </param> - - <conditional name="mir_input"> - <param name="database" type="select" label="Choose Database of miRNAs organisms" help="Choose which database prefer to be used."> - <option value="1" selected="true">MirBase</option> - <option value="2">MirGene</option> - </param> - <when value="1"> - <param name="genome1" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest is not listed, contact the Galaxy team"> - <options from_data_table="n_spiecies" /> - </param> - </when> - <when value="2"> - <param name="genome2" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest is not listed, contact the Galaxy team"> - <options from_data_table="mirgene" /> - </param> - </when> - </conditional> - - - <param name="fal1" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/> - <param name="control" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" /> - <param name="fal2" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/> - <param name="treated" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" /> - - <conditional name="f"> - <param name="fil" type="select" label="Filter low counts" help="Treat genes with very low expression as unexpressed and filter out"> - <option value="1" selected="true">No</option> - <option value="2">Yes</option> - </param> - <when value="2"> - <param name="fil1" type="integer" value="0" label="Minimum percentage of the samples" help="Filter out all genes that do not meet the Minimum counts in at least this many samples of every category"/> - <param name="fil2" type="integer" value="0" label="Minimum counts" help="Filter out all genes that do not meet this minimum count"/> - </when> - <when value="1"> - </when> - </conditional> - - <param name="db" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Database files" /> - <param name="cmatrix" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Output Matrix files, one for each factor level" /> - <param name="c_files" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Count tables, one for each sample" /> - <param name="umis" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Collapsing sam files if samples include UMIs" /> - </inputs> - <outputs> - <collection name="list_output1" type="list" label="Database ${fal1} templated" > - <discover_datasets pattern="__name__" format="tabular" directory="split1" /> - <filter>db == 1 and (analysis == "1" or analysis == "2")</filter> - </collection> - <collection name="list_output2" type="list" label="Database ${fal2} templated" > - <discover_datasets pattern="__name__" format="tabular" directory="split2" /> - <filter>db == 1 and (analysis == "1" or analysis == "2")</filter> - </collection> - <collection name="list_output3" type="list" label="Database ${fal1} non-templated" > - <discover_datasets pattern="__name__" format="tabular" directory="split3" /> - <filter>db == 1 and analysis == "2"</filter> - </collection> - <collection name="list_output4" type="list" label="Database ${fal2} non-templated" > - <discover_datasets pattern="__name__" format="tabular" directory="split4" /> - <filter>db == 1 and analysis == "2"</filter> - </collection> - - <collection name="Counts" type="list" label="Count Matrices" > - <discover_datasets pattern="__name__" format="tabular" directory="Counts" /> - <filter>cmatrix==1</filter> - </collection> - - - <collection name="list_output9" type="list" label="Count files ${fal1} for Differential Expression" > - <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_con" /> - <filter>c_files==1 and (analysis == "1")</filter> - </collection> - <collection name="list_output10" type="list" label="Count files ${fal2} for Differential Expression" > - <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_tre" /> - <filter>c_files==1 and (analysis == "1")</filter> - </collection> - <collection name="list_output11" type="list" label="Count files ${fal1} for Differential Expression" > - <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_con" /> - <filter>c_files==1 and analysis == "2"</filter> - </collection> - <collection name="list_output12" type="list" label="Count files ${fal2} for Differential Expression" > - <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_tre" /> - <filter>c_files==1 and analysis == "2"</filter> - </collection> - - <data name="Results non templated treated1" format="pdf" label="PDF" from_work_dir="$__tool_directory__/report1.pdf" /> - </outputs> - <help> - </help> -</tool>