changeset 6:5506c4307812 draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_tradis_comparison.xml	Wed Oct 23 10:40:28 2019 -0400
@@ -0,0 +1,64 @@
+<tool id="tradis_comparison" name="tradis comparison" version="@VERSION@">
+    <description>Compares two experimental conditions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    #for $counter, $input in enumerate($control):
+            ln -s '$input' $input.element_identifier &&
+            echo  ./$new_name >> control &&
+    #end for
+    
+    #for $counter, $input in enumerate($conditions):
+            ln -s '$input' $input.element_identifier &&
+            echo  ./$new_name >> conditions &&
+    #end for
+
+    tradis_comparison.R 
+    --controls control
+    --conditions conditions
+    -o output.csv
+    -p plot.pdf
+    #if str($filter.filter_selector)=="yes":
+        -f
+        -t $filter.cutoff
+    #end if
+    ]]>    </command>
+    <inputs>
+        <param name="control" type="data" format="csv" multiple="true" label="Control list"/>
+        <param name="conditions" type="data" format="csv" multiple="true" label="Condition list"/>
+        <conditional name="filter">
+            <param name="filter_selector" type="select" label="Filter">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true" >No</option>
+            </param>
+            <when value="yes">
+                <param name="cutoff" type="integer" value="" label="Cut-off value"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output.csv"/>
+        <data name="plot" format="pdf" label="${tool.name} on ${on_string} Plot" from_work_dir="plot.pdf" />
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Adds transposon sequence and quality tags to the read strings and
+        outputs a BAM.
+
+        Usage: add_tags -b file.bam [options]
+
+        Options:
+        -b  : bam file with tradis tags
+        -v  : verbose debugging output
+    ]]>    </help>
+
+</tool>