diff lofreq_alnqual.xml @ 0:d1b53ef02092 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_alnqual.xml	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,78 @@
+<tool id="lofreq_alnqual" name="Add BAQ and IDAQ" version="@WRAPPER_VERSION@0">
+    <description>to BAM with LoFreq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @PREPARE_REF@
+        lofreq alnqual -b $extended $no_baq $no_idaq $recompute_all '$reads' '$reference_fasta_fn' > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="bam" />
+        <expand macro="reference_interface" />
+        <param name="extended" argument="-e" type="boolean" truevalue="-e" falsevalue="" label="Use default instead of extended BAQ" help="Extended BAQ gives better sensitivity with lower specificity" />
+        <param name="no_baq" argument="-B" type="boolean" truevalue="-B" falsevalue="" label="Skip base alignment quality calculation" />
+        <param name="no_idaq" argument="-A" type="boolean" truevalue="-A" falsevalue="" label="Skip indel alignment quality calculation" />
+        <param name="recompute_all" argument="-r" type="boolean" truevalue="-r" falsevalue="" label="Overwrite existing values with computed values" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} to ${on_string}" />
+    </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="output" file="alnqual-out1.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="no_baq" value="true" />
+            <output name="output" file="alnqual-out2.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="no_idaq" value="true" />
+            <output name="output" file="alnqual-out3.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="extended" value="true" />
+            <output name="output" file="alnqual-out4.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="recompute" value="true" />
+            <output name="output" file="alnqual-out5.bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to BAM file
+
+Usage:   lofreq alnqual [options] <aln.bam> <ref.fasta>
+Options:
+         -b       BAM output (instead of SAM)
+         -u       Uncompressed BAM output (for piping)
+         -S       The input is SAM with header
+         -e       Use default instead of extended BAQ (the latter gives better sensitivity but lower specificity)
+         -B       Don't compute base alignment qualities
+         -A       Don't compute indel alignment qualities
+         -r       Recompute i.e. overwrite existing values
+- Output BAM will be written to stdout.
+- Only reads containing indels will contain indel-alignment qualities (tags: ai and ad).
+- Do not change the alignmnent after running this, i.e. use this as last postprocessing step!
+- This program is based on samtools. BAQ was introduced by Heng Li PMID:21320865
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file