# HG changeset patch
# User mvdbeek
# Date 1491428081 14400
# Node ID 44bbb5c4553f490bb340f588f6d2e045c3ef8148
# Parent  8d201345f6dcbfd9dfd9a1597bf4bb13fe6d8bbc
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac

diff -r 8d201345f6dc -r 44bbb5c4553f add_matesequence.xml
--- a/add_matesequence.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/add_matesequence.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.12">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.13">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 8d201345f6dc -r 44bbb5c4553f allow_dovetailing.xml
--- a/allow_dovetailing.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/allow_dovetailing.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.12">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.13">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 8d201345f6dc -r 44bbb5c4553f bam_readtagger.xml
--- a/bam_readtagger.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/bam_readtagger.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.12">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
diff -r 8d201345f6dc -r 44bbb5c4553f findcluster.xml
--- a/findcluster.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/findcluster.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,17 +1,20 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.12">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.13">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+        ln -f -s $input input.bam &&
+        ln -f -s $input.metadata.bam_index input.bam.bai &&
         findcluster
-        --input_path '$input'
+        --input_path input.bam
         #if $reference_fasta:
             --reference_fasta '$reference_fasta'
         #end if
         --output_bam '$output_bam'
         --output_gff '$output_gff'
+        --output_fasta '$output_fasta'
         --sample_name '$input.element_identifier'
         --threads "\${GALAXY_SLOTS:-2}"
     ]]></command>
@@ -21,6 +24,7 @@
     </inputs>
     <outputs>
         <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
+        <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
         <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
     </outputs>
     <tests>
diff -r 8d201345f6dc -r 44bbb5c4553f update_mapq.xml
--- a/update_mapq.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/update_mapq.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.12">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.13">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 8d201345f6dc -r 44bbb5c4553f write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Fri Mar 31 16:28:07 2017 -0400
+++ b/write_supplementary_fastq.xml	Wed Apr 05 17:34:41 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.12">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.13">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.12">readtagger</requirement>
+        <requirement type="package" version="0.3.13">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[