# HG changeset patch
# User mvdbeek
# Date 1522569195 14400
# Node ID 4b1ebfcd0f466a58c2f02f175ca55156d2c6a50d
# Parent  432bb619c079a35f3a174aa716a08ca07d912b01
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d

diff -r 432bb619c079 -r 4b1ebfcd0f46 add_matesequence.xml
--- a/add_matesequence.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/add_matesequence.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.9">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.10">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 432bb619c079 -r 4b1ebfcd0f46 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/allow_dovetailing.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.9">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.10">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 432bb619c079 -r 4b1ebfcd0f46 bam_readtagger.xml
--- a/bam_readtagger.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/bam_readtagger.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.9">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 432bb619c079 -r 4b1ebfcd0f46 filter_insertions.xml
--- a/filter_insertions.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/filter_insertions.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 432bb619c079 -r 4b1ebfcd0f46 findcluster.xml
--- a/findcluster.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/findcluster.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.9">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.10">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -28,33 +28,57 @@
                 --genome_bwa_index '$genome_source.ref_file.fields.path'
             #end if
         #end if
-        --output_bam '$output_bam'
-        --output_gff '$output_gff'
-        --output_fasta '$output_fasta'
+        #if str($make_bam) == 'True':
+            --output_bam '$output_bam'
+        #end if
+        #if str($make_vcf) == 'True'
+             --output_vcf '$output_vcf'
+        #end if
+        #if str($make_gff) == 'True'
+             --output_gff '$output_gff'
+        #end if
+        #if str($make_fasta) == 'True'
+            --output_fasta '$output_fasta'
+        #end if
         --sample_name '$sample_name'
         --threads "\${GALAXY_SLOTS:-2}"
     ]]></command>
     <inputs>
         <param name="input" argument="--input_path" type="data" format="bam"/>
-
+        <param name="make_bam" type="boolean" truevalue="True" checked="true" label="Produce an alignment file containing evidence for insertions."/>
+        <param name="make_vcf" type="boolean" truevalue="True" checked="true" label="Produce a VCF file describing the insertion that have been found."/>
+        <param name="make_gff" type="boolean" truevalue="True" checked="false" label="produce a GFF file describing the insertions that have been found."/>
+        <param name="make_fasta" type="boolean" checked="True" truevalue="True" label="Produce a fasta file containing assembled contigs."/>
         <expand macro="reference_source_conditional" reference_type="transposon"/>
         <expand macro="reference_source_conditional" reference_type="genome"/>
     </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"/>
+        <data name="output_bam" format="bam" label="findcluster BAM on $on_string">
+            <filter>make_bam</filter>
+        </data>
+        <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string">
+            <filter>make_fasta</filter>
+        </data>
+        <data name="output_vcf" format="vcf" label="findcluster VCF on $on_string">
+            <filter>make_vcf</filter>
+        </data>
+        <data name="output_gff" format="gff3" label="findcluster GFF on $on_string">
+            <filter>make_gff</filter>
+        </data>
     </outputs>
     <tests>
         <test>
             <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
+            <param name="make_gff" value="true"/>
             <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
-            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0" sort="True"/>
+            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" compare="sim_size"/>
+            <output name="output_vcf" file="three_cluster_out.vcf" ftype="vcf" compare="sim_size"/>
         </test>
         <test>
             <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
             <param name="transposon_source|reference_source_selector" value="history"/>
             <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
+            <param name="make_gff" value="true"/>
             <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
             <output name="output_gff">
                 <assert_contents>
diff -r 432bb619c079 -r 4b1ebfcd0f46 plot_coverage.xml
--- a/plot_coverage.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/plot_coverage.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.9">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.10">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/a_pasteurianus_tagged_with_dm6_verified.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/all_control_insertions.gff
--- a/test-data/all_control_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
+++ b/test-data/all_control_insertions.gff	Sun Apr 01 03:53:15 2018 -0400
@@ -1,2 +1,3 @@
-X	find_softclip	5p_clip	16727068	16727067	3	+	.	ID=R38_2472;consensus=ACTTAATA;max_mapq=25
-X	find_softclip	3p_clip	16727112	16727111	4	+	.	ID=R38_2473;consensus=TTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAG;max_mapq=28
+TEST	find_softclip	5p_clip	16727068	16727111	6	+	.	ID=softclip_test2;consensus=TTTTTTT
+X	find_softclip	5p_clip	16727068	16727067	3	+	.	ID=softclip_0;consensus=ACTTAATA;max_mapq=25
+X	find_softclip	3p_clip	16727112	16727111	4	+	.	ID=softclip_1;consensus=TTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAG;max_mapq=28
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/all_treatment_insertions.gff
--- a/test-data/all_treatment_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
+++ b/test-data/all_treatment_insertions.gff	Sun Apr 01 03:53:15 2018 -0400
@@ -1,12 +1,13 @@
+TEST	find_softclip	5p_clip	16727068	16727111	6	+	.	ID=softclip_test1;consensus=AAAAAA
 X	feature	predicted_insertion	10766937	10766942	.	+	.	Parent=R37_49;contig_support=2;fraction_full_length=0.03132530120481928;sbjct=RR48388_transposable_element_rover_Gypsy;sbjct_end=7308;sbjct_start=7074;type=predicted_insertion
-X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
-X	find_softclip	5p_clip	10766937	10766936	6	+	.	ID=R37_2667;consensus=GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAG;max_mapq=60
-X	find_softclip	3p_clip	10766943	10766942	3	+	.	ID=R37_2668;consensus=GTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA;max_mapq=60
+X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;softclip_clusters=;total_left_count=6;total_right_count=18;valid_TSD=True
+X	find_softclip	5p_clip	10766937	10766936	6	+	.	ID=softclip_0;consensus=GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAG;max_mapq=60
+X	find_softclip	3p_clip	10766943	10766942	3	+	.	ID=softclip_1;consensus=GTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA;max_mapq=60
 X	feature	left_insert	16726713	16727261	.	+	.	Parent=R37_26;fraction_full_length=0.003280519299225239;read_support=1;sbjct=FBti0059747_gtwin_Gypsy;sbjct_end=2536;sbjct_start=2489;type=left_insert
-X	findcluster	gtwin	16726713	16727261	1	+	.	ID=R37_26;genotype=reference;genotype_likelihoods=1.0,1.93425522512e-14,6.88207144991e-72;insert_reference_name=gtwin;left_inserts=;left_mate_count=0;max_mapq=60;nref=47;right_inserts=;right_mate_count=1;total_left_count=0;total_right_count=1;valid_TSD=False
+X	findcluster	gtwin	16726713	16727261	1	+	.	ID=R37_26;genotype=reference;genotype_likelihoods=1.0,1.93425522512e-14,6.88207144991e-72;insert_reference_name=gtwin;left_inserts=;left_mate_count=0;max_mapq=60;nref=47;right_inserts=;right_mate_count=1;softclip_clusters=;total_left_count=0;total_right_count=1;valid_TSD=False
 X	feature	left_insert	16727068	16727111	.	+	.	Parent=R37_27;fraction_full_length=0.6875;read_support=1;sbjct=FBti0062261_jockey2_Jockey;sbjct_end=63;sbjct_start=19;type=left_insert
 X	feature	right_insert	16727068	16727111	.	+	.	Parent=R37_27;fraction_full_length=0.0017704870646047116;read_support=1;sbjct=FBti0062666_HMS-Beagle_Gypsy;sbjct_end=10537;sbjct_start=10488;type=right_insert
-X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
-X	find_softclip	3p_clip	16727068	16727111	6	+	.	Parent=R37_27;consensus=TTTAATAAAATTAAAGGAC;max_mapq=34
-X	find_softclip	5p_clip	16727068	16727111	5	+	.	Parent=R37_27;consensus=GAATTTAATATTTAAAAAGGTGGACTGAATACTTAATA;max_mapq=34
-X	find_softclip	3p_clip	16727110	16727109	1	+	.	ID=R37_2929;consensus=CCTTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAGAAAATAATATTAAGTCTTTAAAAG;max_mapq=34
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True
+X	find_softclip	3p_clip	16727068	16727111	6	+	.	ID=softclip_2;consensus=TTTAATAAAATTAAAGGAC;max_mapq=34
+X	find_softclip	5p_clip	16727068	16727111	5	+	.	ID=softclip_3;consensus=GAATTTAATATTTAAAAAGGTGGACTGAATACTTAATA;max_mapq=34
+X	find_softclip	3p_clip	16727110	16727109	1	+	.	ID=softclip_4;consensus=CCTTTAATAAAATTAAAGGACAACTAAACGGAAGGAAAATATCGTGAGCAGAAAATAATATTAAGTCTTTAAAAG;max_mapq=34
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/confirmed_insertions.gff
--- a/test-data/confirmed_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
+++ b/test-data/confirmed_insertions.gff	Sun Apr 01 03:53:15 2018 -0400
@@ -1,3 +1,4 @@
-TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
+2R	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
+TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
 X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
-X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_in_control
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_in_control
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6.bam
Binary file test-data/dm6.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_mate_annotated.bam
Binary file test-data/dm6_mate_annotated.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/dm6_tagged_with_a_pasteurianus_verified.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_discard_out.bam
Binary file test-data/proper_pair_discard_out.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_discard_verified_empty.bam
Binary file test-data/proper_pair_discard_verified_empty.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/proper_pair_out_suboptimal_tags.bam
Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/putative_insertions.gff
--- a/test-data/putative_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
+++ b/test-data/putative_insertions.gff	Sun Apr 01 03:53:15 2018 -0400
@@ -1,3 +1,4 @@
-TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
+2R	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
+TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;softclip_clusters=softclip_test1
 X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
-X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
+X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.bam
Binary file test-data/three_cluster_out.bam has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Thu Mar 15 07:20:58 2018 -0400
+++ b/test-data/three_cluster_out.gff	Sun Apr 01 03:53:15 2018 -0400
@@ -1,8 +1,8 @@
 ##gff-version 3
-3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;total_left_count=2;total_right_count=0;valid_TSD=False
-3R	find_softclip	3p_clip	13373515	13373524	7	+	.	Parent=extended_and_annotated_roi.bam_1;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;max_mapq=60
-3R	find_softclip	5p_clip	13373515	13373524	6	+	.	Parent=extended_and_annotated_roi.bam_1;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
-3R	findcluster	TE	13373515	13373524	20	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=6.2761999508986e-30,1.9073449948406318e-06,0.9999980926550052;insert_reference_name=None;left_inserts=0,GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;total_left_count=9;total_right_count=11;valid_TSD=False
-3R	findcluster	TE	13374539	13374676	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=homozygous;genotype_likelihoods=0.21259842519685054,0.3937007874015747;insert_reference_name=None;left_inserts=;left_mate_count=0;max_mapq=60;nref=0;right_inserts=;right_mate_count=1;total_left_count=0;total_right_count=1;valid_TSD=False
-3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;total_left_count=2;total_right_count=0;valid_TSD=False
-3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=extended_and_annotated_roi.bam_4;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
+3R	findcluster	TE	13373206	13373206	2	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	3p_clip	13373515	13373514	7	+	.	ID=SOFTCLIP_8392192716115976782;consensus=ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC;max_mapq=60
+3R	findcluster	TE	13373515	13373524	20	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=6.2761999508986e-30,1.9073449948406318e-06,0.9999980926550052;insert_reference_name=None;left_inserts=GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG;left_mate_count=6;max_mapq=60;nref=0;right_inserts=GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_count=6;softclip_clusters=SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485;total_left_count=9;total_right_count=11;valid_TSD=False
+3R	find_softclip	5p_clip	13373525	13373524	6	+	.	ID=SOFTCLIP_3495167510329773485;consensus=CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT;max_mapq=60
+3R	findcluster	TE	13374539	13374676	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=homozygous;genotype_likelihoods=0.21259842519685054,0.3937007874015747;insert_reference_name=None;left_inserts=;left_mate_count=0;max_mapq=60;nref=0;right_inserts=;right_mate_count=1;softclip_clusters=;total_left_count=0;total_right_count=1;valid_TSD=False
+3R	findcluster	TE	13374595	13374709	2	+	.	ID=extended_and_annotated_roi.bam_3;genotype=homozygous;genotype_likelihoods=0.010684606252473286,0.32977179791584216,0.6595435958316843;insert_reference_name=None;left_inserts=GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_count=2;max_mapq=60;nref=0;right_inserts=;right_mate_count=0;softclip_clusters=;total_left_count=2;total_right_count=0;valid_TSD=False
+3R	find_softclip	5p_clip	13374677	13374676	1	+	.	ID=SOFTCLIP_2520711244791099460;consensus=TGGCAAAACATATGCAAAGTGCA;max_mapq=60
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_cluster_out.vcf	Sun Apr 01 03:53:15 2018 -0400
@@ -0,0 +1,1916 @@
+##fileformat=VCFv4.1
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+##contig=<ID=mitochondrion_genome,length=19524>
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Maximum MAPQ of evidence supporting the variant">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DEL:ME,Description="Deletion of mobile element present in reference">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=INS:ME,Description="Insertion of mobile element">
+##ALT=<ID=SOFTCLIP,Description="Softclipped alignments">
+##ALT=<ID=SOFTCLIP:5P,Description="Softclipped alignments where softclipping removes the 5p side">
+##ALT=<ID=SOFTCLIP:3P,Description="Softclipped alignments where softclipping removes the 3p side">
+##FORMAT=<ID=MENAME,Number=1,Type=String,Description="Mobile element name">
+##FORMAT=<ID=MESTART,Number=1,Type=Integer,Description="Mobile element reference start">
+##FORMAT=<ID=MEEND,Number=1,Type=Integer,Description="Mobile element reference end">
+##FORMAT=<ID=MEASSEMBLY5,Number=.,Type=String,Description="Sequences assembled at 5p breakpoint of mobile element insertion">
+##FORMAT=<ID=MEASSEMBLY3,Number=.,Type=String,Description="Sequences assembled at 3p breakpoint of mobile element insertion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=SU5,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant from the 5p side">
+##FORMAT=<ID=SU3,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant form the 3p side">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=PE5,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant from the 5p side">
+##FORMAT=<ID=PE3,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant from the 3p side">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=SR5,Number=1,Type=Integer,Description="Number of split reads supporting the variant from the 5p side">
+##FORMAT=<ID=SR3,Number=1,Type=Integer,Description="Number of split reads supporting the variant from the 3p side">
+##FORMAT=<ID=MSP,Number=1,Type=Integer,Description="Number of fragments supporting insertion with both mates. Indicates short insertions.">
+##FORMAT=<ID=CLIP_CONSENSUS,Number=1,Type=String,Description="Consensus sequence for SOFTCLIP event. The consensus is listed in the 5p to 3p direction relative to the alignment.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	extended_and_annotated_roi.bam
+3R	13373206	INS_2444456283915041025	N	<INS:ME>	.	.	END=13373207;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2444456283915041025;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.::
+3R	13373515	INS_630831370416389201	N	<INS:ME>	.	.	END=13373525;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_630831370416389201;MATEID=SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485,SOFTCLIP_8392192716115976782,SOFTCLIP_3495167510329773485	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:6.2762e-30,1.90734e-06,0.999998:0,20:20:20:9:11:8:3:5:0::.:.:GGAAAAATAACGGTATGGATGCACAACAAATCATGCGCTTAAGTGTAAGTAAAAATGTAAGCTGGTTTGATGTGTTTATGCATGTGCAAGATTGTATGTACAATTAGTGTAAGTATGTAAACGTAATATGAGAAGCATATTATGTTACTATATGTATATGTCCATATGTCCATATGCATACGAATTGGCGCACTTGCTTATATTTGATATGAGTTTGTTAGTTAGATACATTCCGAG:GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG
+3R	13373515	SOFTCLIP_8392192716115976782	N	<SOFTCLIP:3P>	.	.	END=13373514;SVTYPE=<SOFTCLIP:3P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201	CLIP_CONSENSUS:AD:SU	ACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTAC:0,7:7
+3R	13373525	SOFTCLIP_3495167510329773485	N	<SOFTCLIP:5P>	.	.	END=13373524;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT=INS_630831370416389201;MATEID=INS_630831370416389201	CLIP_CONSENSUS:AD:SU	CTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGT:0,6:6
+3R	13374539	INS_2520711244791099460	N	<INS:ME>	.	.	END=13374677;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_2520711244791099460;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.212598,0.393701,0.393701:0,1:1:1:0:1:0:0:0:0::.:.::
+3R	13374595	INS_7083183827793206730	N	<INS:ME>	.	.	END=13374710;SVTYPE=INS:ME;SVLEN=.;MQ=60;EVENT=INS_7083183827793206730;MATEID	GT:GL:AD:DP:SU:SU5:SU3:SR:SR5:SR3:MSP:MENAME:MESTART:MEEND:MEASSEMBLY5:MEASSEMBLY3	1/1:0.0106846,0.329772,0.659544:0,2:2:2:2:0:0:0:0:0::.:.:GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG:
+3R	13374677	SOFTCLIP_2520711244791099460	N	<SOFTCLIP:5P>	.	.	END=13374676;SVTYPE=<SOFTCLIP:5P>;MQ=60;EVENT;MATEID	CLIP_CONSENSUS:AD:SU	TGGCAAAACATATGCAAAGTGCA:0,1:1
diff -r 432bb619c079 -r 4b1ebfcd0f46 test-data/three_cluster_plot.pdf
Binary file test-data/three_cluster_plot.pdf has changed
diff -r 432bb619c079 -r 4b1ebfcd0f46 update_mapq.xml
--- a/update_mapq.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/update_mapq.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.9">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.10">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 432bb619c079 -r 4b1ebfcd0f46 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Thu Mar 15 07:20:58 2018 -0400
+++ b/write_supplementary_fastq.xml	Sun Apr 01 03:53:15 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.9">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.10">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.9">readtagger</requirement>
+        <requirement type="package" version="0.4.10">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[