# HG changeset patch
# User glogobyte
# Date 1603872810 0
# Node ID d2eea02053a071f29d2359afa13f958d932887bc
# Parent  d766563ab56d4916120da2f1ca233377bf27d49a
Deleted selected files

diff -r d766563ab56d -r d2eea02053a0 toolExample_v2.xml
--- 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>