--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoread.xml	Wed Oct 13 16:03:19 2021 +0000
@@ -0,0 +1,127 @@
+
+<tool id="IsoRead" name="IsoRead: miR and isomiR identification and classification" version="0.1.0">
+  <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.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
+      #end if
+      #if $f.fil == "2":
+        #set path=$mir_input.genome1.fields.path
+        python -W ignore $__tool_directory__/mirbase.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "$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.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
+      #end if
+      #if $f.fil == "2":
+        #set path=$mir_input.genome2.fields.value
+        python -W ignore $__tool_directory__/mirgene.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "$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="Reference miRNA DB" 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 are not listed, contact the Galaxy team">
+         <options from_data_table="mirbase" />
+        </param>
+     </when>
+     <when value="2">
+        <param name="genome2" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest are 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" />
+  </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 ${fal2} for Differential Expression" >
+        <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_tre" />
+        <filter>c_files==1 and analysis == "2"</filter>
+    </collection>
+  
+    <data name="Results non templated treated1" format="pdf" label="IsomiR Profile Report" from_work_dir="$__tool_directory__/report1.pdf" />
+  </outputs>
+  <help>
+  </help>
+</tool>