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changeset 3:67f6938b3c42 draft

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Uploaded
author glogobyte
date Fri, 16 Oct 2020 12:17:22 +0000
parents c607e8513b5b
children 2b231cde4efd
files toolExample.xml
diffstat 1 files changed, 199 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolExample.xml	Fri Oct 16 12:17:22 2020 +0000
@@ -0,0 +1,199 @@
+
+<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
+
+    <!--
+    #if $mir_input.database == "1" and $f.filter == "2":
+      #set path=$mir_input.genome1.fields.path
+      python -W ignore $__tool_directory__/mirbase_ultra_v1.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "$filters.fil1" -counts "$filter.fil2 -name1 $fal1 -name2 $fal2"
+    #else:
+      #set path=$mir_input.genome2.fields.value
+      python -W ignore $__tool_directory__/main_galaxy_mirgene.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -program $program -f "$mir_input.database" -percentage "$filters.fil1" -counts "$filters.fil2" ->
+    #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>
+    <!--param name="program" type="select" label="Choose differential expression/statistics module" help="Choose the category of miRNAs for detection">
+      <option value="0" selected="true">Deseq2</option>
+      <option value="1">EdgeR</option>
+      <option value="2">Deseq2 and EdgeR</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 ${fal2} non-templated" >
+        <discover_datasets pattern="__name__" format="tabular" directory="split4" />
+        <filter>db == 1 and analysis == "2"</filter> 
+    </collection>
+   
+    <!--
+    <data name="Results non templated control" format="tabular" label="${fal1} matrix counts of non templated results" from_work_dir="$__tool_directory__/Deseq_final_non_LH2E">
+      <filter>cmatrix==1 and analysis == "2"</filter>
+    </data>
+    <data name="Results non templated treated" format="tabular" label="${fal2} matrix counts of non templated results" from_work_dir="$__tool_directory__/Deseq_final_non_LH8E">
+      <filter>cmatrix==1 and analysis == "2"</filter>
+    </data>
+    <data name="Results templated control" format="tabular" label="${fal1} matrix counts of templated results" from_work_dir="$__tool_directory__/Deseq_final_temp_LH2E">
+      <filter>cmatrix==1</filter>
+    </data>
+    <data name="Results templated treated" format="tabular" label="${fal2} matrix counts of templated results" from_work_dir="$__tool_directory__/Deseq_final_temp_LH8E">
+       <filter>cmatrix==1</filter>
+    </data>
+    -->
+    <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>
+  
+
+    <!--
+    <collection name="list_output13" type="list" label="EdgeR count files ${fal1} templated" >
+        <discover_datasets pattern="__name__" format="tabular" directory="Edger/split5"  />
+        <filter>c_files==1 and (program=="1" or program=="2" ) and (analysis == "1")</filter>
+    </collection>
+    <collection name="list_output14" type="list" label="EdgeR count files ${fal2} templated" >
+        <discover_datasets pattern="__name__" format="tabular" directory="Edger/split6" />
+        <filter>c_files==1 and (program=="1" or program=="2") and (analysis == "1")</filter>
+    </collection>
+    <collection name="list_output15" type="list" label="EdgeR count files ${fal1}" >
+        <discover_datasets pattern="__name__" format="tabular" directory="Edger/split7" />
+        <filter>c_files==1 and (program=="1" or program=="2") and analysis == "2"</filter>
+    </collection>
+    <collection name="list_output16" type="list" label="EdgeR count files ${fal2}" >
+        <discover_datasets pattern="__name__" format="tabular" directory="Edger/split8" />
+        <filter>c_files==1 and (program=="1" or program=="2") and analysis == "2"</filter>
+    </collection>
+    -->
+
+    <!--data name="O" format="png" label="c_hist" from_work_dir="$__tool_direcory__/c_hist_red.png"/-->
+    <!--data name="O1" format="png" label="t_hist" from_work_dir="$__tool_direcory__/t_hist_red.png"/-->
+    <!--data name="OOOOOOOOO" format="png" label="c_non-hist" from_work_dir="$__tool_direcory__/c_hist_non_red.png"/-->
+    <!--data name="SSSSSSSSS" format="png" label="t_non-hist" from_work_dir="$__tool_direcory__/t_hist_non_red.png"/-->
+    <!--data name="OOOOOOOOO111" format="png" label="non-pie" from_work_dir="$__tool_direcory__/pie2.png"/-->
+    <!--data name="SSSSSSSSS1" format="png" label="pie" from_work_dir="$__tool_direcory__/pie1.png"/-->
+    <!--data name="OOOOO" format="png" label="spider1" from_work_dir="$__tool_direcory__/spider1.png"/-->
+    <!--data name="OOOOOO" format="png" label="spider2" from_work_dir="$__tool_direcory__/spider2.png"/-->
+    <!--data name="OOo" format="png" label="WWW" from_work_dir="$__tool_direcory__/bar2.png"/-->
+    <!--data name="OOOOOOOOO1" format="png" label="WWWWWWW" from_work_dir="$__tool_direcory__/bar1.png"/-->
+    <!--data name="OO" format="png" label="logo1" from_work_dir="$__tool_direcory__/logo1.png"/-->
+    <!--data name="O5" format="png" label="logo2" from_work_dir="$__tool_direcory__/logo2.png"/-->
+    <data name="Results non templated treated1" format="pdf" label="PDF" from_work_dir="$__tool_directory__/report1.pdf" />
+    <!--data name="Results" format="png" label="results2" from_work_dir="$__tool_directory__/w.png"/-->
+    <data name="Results non templated treated3" format="tabular" label="results3" from_work_dir="$__tool_directory__/LH8E" />
+    <!--data name="Results non templated treated4" format="tabular" label="results4" from_work_dir="$__tool_directory__/Deseq_final_temp_LH8E"/-->
+  </outputs>
+  <help>
+  </help>
+</tool>