diff lofreq_viterbi.xml @ 0:33a416e1659e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_viterbi.xml	Tue Dec 17 17:25:37 2019 -0500
@@ -0,0 +1,51 @@
+<tool id="lofreq_viterbi" name="Realign reads" version="@WRAPPER_VERSION@0" python_template_version="3.5">
+    <description>with LoFreq viterbi</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.9">samtools</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+        @PREPARE_REF@
+        lofreq viterbi --ref '$reference_fasta_fn' --out - $keepflags --defqual $defqual '$reads' | samtools sort - -O BAM -o '$realigned'
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="bam" label="Reads to realign" />
+        <expand macro="reference_interface" />
+        <param argument="--keepflags" type="boolean" truevalue="--keepflags" label="Don't delete flags MC, MD, NM, and A" help="These flags are all prone to changing during realignment" />
+        <param argument="--defqual" type="integer" value="-1" label="Quality to assume for all bases with BQ2" />
+    </inputs>
+    <outputs>
+        <data name="realigned" format="bam" label="${tool.name} on ${on_string}: Realigned reads" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <output name="realigned" file="viterbi-out1.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="keepflags" value="true" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <output name="realigned" file="viterbi-out2.bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Usage: lofreq viterbi [options] in.bam
+
+Options:
+    -f | --ref FILE     Indexed reference fasta file [null]
+    -k | --keepflags    Don't delete flags MC, MD, NM and A, which are all prone to change during realignment.
+    -q | --defqual INT  Assume INT as quality for all bases with BQ2. Default (=-1) is to use median quality of bases in read.
+    -o | --out FILE     Output BAM file [- = stdout = default]
+    --verbose      Be verbose
+
+NOTE: Output BAM file will (likely) be unsorted (use samtools sort, e.g. lofreq viterbi ... | samtools sort -')
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file