diff biotradis_filter_tags.xml @ 0:afe9a515d145 draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_filter_tags.xml	Thu Jul 25 06:03:12 2019 -0400
@@ -0,0 +1,36 @@
+<tool id="filter_tradis_tags" name="filter tradis tags" version="@VERSION@">
+    <description>Filters a BAM file and outputs reads with tag matching -t option.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    
+    filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered
+
+    ]]></command>
+    <inputs>
+         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
+         <param name="tag" type="text" label="Tags to filter" help="" />
+         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
+         <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
+    </inputs>
+
+    <outputs>
+       <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" />
+    </outputs>
+
+    <!-- <tests>
+    </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>