diff ivar_filtervariants.xml @ 0:c88553ec696e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_filtervariants.xml	Mon Mar 30 07:18:00 2020 -0400
@@ -0,0 +1,45 @@
+<tool id="ivar_filtervariants" name="ivar filtervariants" version="@VERSION@+galaxy0">
+    <description>Filter variants across replicates or multiple samples aligned using the same reference</description>
+        <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        #for $counter, $input in enumerate($inputs):
+            ln -s '$input' ./var_${counter}.tsv &&
+        #end for
+        ivar filtervariants 
+        -p filtered.tsv
+        #for $counter, $input in enumerate($inputs)
+            ./var_${counter}.tsv
+        #end for
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="tabular" multiple="true" label="Variant tsv files for each replicate"/>
+    </inputs>
+    <outputs>
+        <data name="output_filtered" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="filtered.tsv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="zika/Z52_a.tsv,zika/Z52_b.tsv" ftype="tabular"/>
+            <output name="output_filtered" file="zika/Z52.tsv" ftype="tabular" lines_diff="10"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        iVar can be used to get an intersection of variants(in .tsv files) called
+        from any number of replicates or from different samples using the same
+        reference sequence. This intersection will filter out any iSNVs that do not
+        occur in a minimum fraction of the files supplied. This parameter can be
+        changed using the -t flag which range from 0 to 1 (default). Fields that are
+        different across replicates(fields apart from REGION, POS, REF, ALT,
+        REF_CODON, REF_AA, ALT_CODON, ALT_AA) will have the filename added as a
+        suffix. If there are a large number of files to be filtered, the -f flag can
+        be used to supply a text file with one sample/replicate variant .tsv file
+        per line.
+        
+        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+    ]]></help>
+<expand macro="citations" />
+</tool>