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Changeset 70:f383ca1c5033 (2019-11-05)

Previous changeset 69:97411db5f752 (2019-09-05) Next changeset 71:b090e190c813 (2019-12-18)

Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"

modified:
add_matesequence.xml
allow_dovetailing.xml
bam_readtagger.xml
extract_variants.xml
filter_insertions.xml
findcluster.xml
plot_coverage.xml
update_mapq.xml
write_supplementary_fastq.xml

added:
normalize_readsizes.xml
test-data/long_insert_tagged.tab
test-data/long_reads_a.fastq
test-data/long_reads_a_normalized.fastq
test-data/long_reads_b.fastq
test-data/long_reads_b_normalized.fastq

diff -r 97411db5f752 -r f383ca1c5033 add_matesequence.xml
--- a/add_matesequence.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/add_matesequence.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.16">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.17">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[

diff -r 97411db5f752 -r f383ca1c5033 allow_dovetailing.xml
--- a/allow_dovetailing.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/allow_dovetailing.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.16">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.17">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'

diff -r 97411db5f752 -r f383ca1c5033 bam_readtagger.xml
--- a/bam_readtagger.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/bam_readtagger.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.16">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.17">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s

diff -r 97411db5f752 -r f383ca1c5033 extract_variants.xml
--- a/extract_variants.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/extract_variants.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,12 +1,13 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.16">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.17">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
ln -fs '$insert_reference.fields.path' reference.fa &&
-extract_variants '$input' '$output' reference.fa
+extract_variants '$input' '$output_alignment' reference.fa &&
+summarize_fragments '$output_alignment' '$output_tabular'
     ]]></command>
     <inputs>
         <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
@@ -15,13 +16,15 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output" format_source="input"/>
+        <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
+        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
     </outputs>
     <tests>
         <test>
             <param name="input" value="long_insertion.bam" ftype="bam"/>
             <param name="insert_reference" value="transposon"/>
-            <output name="output" file="long_insert_tagged.bam" ftype="bam"/>
+            <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
+            <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[

diff -r 97411db5f752 -r f383ca1c5033 filter_insertions.xml
--- a/filter_insertions.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/filter_insertions.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.16">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.17">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[

diff -r 97411db5f752 -r f383ca1c5033 findcluster.xml
--- a/findcluster.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/findcluster.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.16">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.17">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[

diff -r 97411db5f752 -r f383ca1c5033 normalize_readsizes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_readsizes.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -0,0 +1,45 @@
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17">
+    <description>of multiple fastq files</description>
+    <requirements>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
+    </requirements>
+    <version_command>normalize_readsizes --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+#for $i, $element in enumerate($input):
+    ln -fs '$element' '${i}.${element.ext}' &&
+#end for
+normalize_readsizes
+#for $i, $element in enumerate($input):
+    -i '${i}.${element.ext}'
+    -o '${i}.out.${element.ext}'
+#end for
+#for $i, $element in enumerate($output):
+    && mv '${i}.out.${element.ext}' '$element'
+#end for
+    ]]></command>
+    <inputs>
+        <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/>
+    </inputs>
+    <outputs>
+        <collection name="output" type="list" structured_like="input" inherit_format="true"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input">
+                <collection type="list">
+                  <element name="a" value="long_reads_a.fastq" />
+                  <element name="b" value="long_reads_b.fastq" />
+                </collection>
+            </param>
+            <param name="insert_reference" value="transposon"/>
+            <output_collection name="output">
+                <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/>
+                <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same
+across all datasets.
+    ]]></help>
+</tool>

diff -r 97411db5f752 -r f383ca1c5033 plot_coverage.xml
--- a/plot_coverage.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/plot_coverage.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.16">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.17">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re

diff -r 97411db5f752 -r f383ca1c5033 test-data/long_insert_tagged.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/long_insert_tagged.tab Tue Nov 05 05:06:18 2019 -0500

@@ -0,0 +1,2 @@
+reference start end insert_reference insert_start insert_end insert_orientation query_start query_end query_length read_length query_name evidence_type
+3R 18395207 18395209 F-element 2417 4708 + 0 2285 2285 2319 long_insert insert

diff -r 97411db5f752 -r f383ca1c5033 test-data/long_reads_a.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/long_reads_a.fastq Tue Nov 05 05:06:18 2019 -0500

b'@@ -0,0 +1,24 @@\n+@db38c012-58da-4dc8-88b7-c73a45199d01\n+AATCCTCACTGTTTCGACCTGGTCCGGCCAACTCGCATCCAGCTGTTCCCAATAACTGAAATTCTTTCTTTCTAATCGGGAACCAGGTAGCATAGAAATATGCCAATAACATGAGAAAGTCAGGCATTTTTCTGCAGCCAAAGCCAAGGCGCCACGATGGCAACAAAGCTGCTAAGTAGCAGTGGATGATGGTGAGAGTGGTGGGCATGGATGTTGTTGTTTTCGATCTTGCCGGCGAGCAGTGACAGCAGCAACAACAAGCTCCAATGGGTCCAGTGTGCGAGTGTTTGCCAGTGGCAGAACCACATTTTGCAAACCGGCCTCTAACGACCTGCATTTGACAAAACATGATCGGTTTAACACCGTCTCTGTCTCCAGCATCTCCATCATCAGAACCTCTCTTTCTGTTGGCCATCTCGGAGTTTAGTTGGCCAGCTTGGAGAACGAATCTGCCGCTCTAGACGCGGAGTGAATGGTAATGTCAATCTTGTGGTTTTATGGTCATGTGTATTTTGTCACTTGTGGGCTACGGCTCAAATTATCAATTGGACTTGGCATGTCAGGTGGAATCGGAATCGAAATTCGCTTTGGGCTTCGAACGGTTTGCCAAGAATTTGCAGAGAATGGAAAGGGTTGGCAGACCTGTATGAAAATATTTGGCCAAATCTGGTTTGCCCATTGCTCTAGAATTCCATATTAACGAGAGTGAATTTATTTGGTTAAAGTTATGCGCACTAAAATAATGATTCAATTTGCTGATTTGCTAGCGATCGTAAATCCCTTATTAATATTAATACAGAAATTGAAGTAAATGCTATAAATATTTCCCACTTCCACAATAACTTTATTTTGTTTGCATTAATATTAATTCCGTCGTCTAGTTAATATTTATCAATCAACGACTGTATTCCTCTAATCACATGTTTACCCATTTTCAGCAGACAAATTTAATTTGCAAATTCATAAAGTCCTGCTCAATTGTGTGGCTGAGGGAGATCCTCCGCTCGAAAATCGTTTAAAATCATAAGCCATTAAGTGCGAATTCAGCAGTTCAGCATGTAATATTCGCATAAAGCGAAAATTTGTGGTCTTTTCGGAGGTGGGTGATTACCATTTCCTCTAGGTTTCCCCTGACGATTTTAATTCCTTTCTATGCACGAGCGTATATTCATATATGCTTATTTAGACAATAAACGCGCATTCGTAAAGTTTCGACTTAAATGGCTGGTTATTCCCCAGACAGATTTACATTACGGGGCCAGTTAGCGAGCATTATTTATCAGCTTTATGCGTTCAAGCCCCGATCGATTACAGCTTAACGCCTTGCACGCTCCACTGGCCAGCAGCGTTTTCGTTTGGTGAACCCTAAGAGCGCCCCGCGTCGAAGAGAAATCGCGTCGAACACCACGGGTCGAATTCGATTTCATGAACTTTAATGAGTCGCGCGACAGATCCCCAGCGCGATGCGACAGAGATGCGAACAATACGGCCGCTGCGGAGAGACGGTTATACACCGTTGGCGCCTTTCCGGTAAAGGTGGCGCCAGTATCGGTATCTTTTTGCGACTTTTGCTTGTTTTTTTATTCTGCTGCTGCTTTTAATTTCGGTTACGCCCACTTGACGACGGCAGGCAGCAGCAACAATGGAAATAATAACAACAACGAAGCGAAGCTTAGCCGCAGGCAGAAAAAAGATTCAGCGACGATCGATCCAGATCGATCAGTTTGGATCGTTGGATCACGCTTGGATCGCATGGATCGTTTCGAGCTTGGATCGCTGCGATTGATCGGTCAGCTTCAGCCTGAACGCTGCCGCTCAAATTGGGCAGCGGCGTTTAGCAGCCGCAGCGCTAAATTAGCAACAGGTTCACGACAGCGGTACAGTGAAGAATACCGGGGACGCAACTATTTTAAAATCAAAAGCTCACCAAGTCCCATTTAATTCGTGTTTCTATGCTAGAGTTGTCGGAATATGATAACAGGAATACGCTTATGATCGAAAATCTAAATTGAAATTGAATTAATTTAAATTTCTAAATATTTTCGCTGCGTGTTAGCCCTGCCCGCAACCCCTTCCACCACCAGCCACCTCCACCTGTTTCACCGCGCGACCACTCTCTTTTCATCGATCAGACAGATGAGCACGCGCTCGCTTAATGACGACACGAAGCCGCCGTTTGAGCCGCGACAGAAGGAAAGAGATGGCGGCATGCTGGGCGAAAGAGAATAACGCTGCTGCTGGCGACGAAAAATCACGGCGGCGGCGCCAGTGTTTGTCAAACGATCGAGTGCCGAGATCGAATACCACTACCAATGCCGATGCCCGTGGTGCCCGTGATACCCGTCACGGCGGATGACGGCAAAACCCGTTTGACGACCTTGGATGTAAAAATTCACCAGCGGAAGAAGAGAGAGAGTGAGACGCAGGCTGGCAAGAGGAAAGGAGCGAGAAGCCAAACAAATGCAAACATACTCAAACATTCCGACAGATTCCGGCAATATCTTACACTCTTTTCCTGCTACACAGAGGGCATTATTTCCTATCATATCATGAAATTTGAAGAACAGTCTAACCGCTTGTAGATTGCTTCAATTTCTTCACGCCTCATAACTAAACTGGCAGTCTGCTCAAATATTCGAGCATTTTCGGTTATTTTCATTTTGGCAGCCCGCAAAGGGATGTTGCTGCAATATAAAGAGTCTGAATGTCCTGCTGGCTGGACACTGGCGTCGTCCATACTGAGAGGGAGACAGATATGGTGGCGAGAAAGGGCGGAAAACACTTGGCGAGTACAAAGTTTGTTTTAGCAAACGTGTTTGTACTTCTATTTCATTCGTTTCATTTCGCTTTAAGTGACTTTTATCGAGGCCAAAAGCAGCTCCACTCGCCAACTTGGCAGGATCTATGGAGCCTTTATGAAGGAGGGTGGGGAGGGCAGTGGAGTCGGTATAAATGCAGAAATTAAAAAGTGGCAGAAAGCGACCTCGAGTCGACTCACCTGGCATTCGCACTTGAAACGGGTGAAAATCTGCGGCTGGTTCTTCGGTTGGACTTCTTCTCCTCATTCGAAGACGGGATTGCCGGACGCCTGTGAAAGAGGTGGAACTCCGATTAATGAGGTATTGCTATGTGGGTGGTGGGTTGGGTAATGGTGGTGCCCTCTTGGACCCCGACCTCGACCCCCACCACGGCATTTCCTGCCTCTGGCGTTGACTCTTTGTTTTAATGTACAGAGCAAACACAAAACAAGACGATTCGTACGTGTACAAACGCCGGAATTGCCACCGGCCGAGATCTTATCCGACCACGTGATGACCCAAAATGGACTCGCCCACCCTCCGCAACCTCGTCCGCTTGCATCTCAATCCTGATCTCCCTCTGCAGGTCAATGAGATTGGGCCTCTGGATTTATGTATGTATGTACATATGTGTGGCGTATTATTATTAATGCAAGCGTGTTTTATCTACACGGTGAAAAGATTTTATCAGGGATATGTGCCGTTGGGCAGAAATATGTGTAGATACCTTTCGTTCAGTTCTTGGTGATTTTCCAAAATATGTTCTATTAAGATTCTAAGATTTATAATCAAACTCCTAACTATTTATGTGACTATAAATTAATCAGTATTTTTCCCAGTGTAAGTACCCTTCTGCCTCAATCTGTTGTAGTTGCCACTTTGTTTGCTTTTAACTATCTCCCTTTTTGGTGGCATAGGAGGGTCAAAAGTAATGAAAGCGTTGCATGGTAAACATGTTGCTAACAATAATAACAACAACAACAATCAACAATGCGAGACAGAAAAGATGAAGCGGAAGTAATCGAGAGAAGGAGCGAGACGGAAGGCAGGTGGCTTATTGCGGCGAGTAGGGAATGGAGACTTTACGATCCCAGCGGGCTGGAGCCGCTCTTCTTCTTCTTCTTCCTCCCTCTAAAATGCGAGG'..b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diff -r 97411db5f752 -r f383ca1c5033 test-data/long_reads_a_normalized.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/long_reads_a_normalized.fastq Tue Nov 05 05:06:18 2019 -0500

diff -r 97411db5f752 -r f383ca1c5033 test-data/long_reads_b.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/long_reads_b.fastq Tue Nov 05 05:06:18 2019 -0500

b'@@ -0,0 +1,24 @@\n+@29c296f1-2879-4ae7-afc7-55e36d5d1108\n+AACAGTCAGACAAATAATTAAGTATAGAACCAAAATAGTATCATCACTTGGAATCTAAACAACACTATCATAGAACAAGAATTGCCAGAAATAAATAAAATGAAGCAGTTGGCAACAAAATGTAACAATGAAAACAAATGTAAAATCAAAATATGGTATAATACTTAACGAAAACAAACTAAGTAGAGATAAACCTTACCCCATTGTACACCTTAAGCTATTAAAATAAAACCAATAGAACTTATGGGACATTGTACAATTAATATCAAATAATAATATCCACAGTTTGTATAATAGTATCAATCCTCAAGCCTCATCTTGTATTGCTTGTATTTGCCAAAACTAAAAACAAAATAATCCATTTGAATCACAAGATGCAAATCCAACTGCATCACCAGATTGCAGGGCATCAGCACCAATAGAGTGGAAGCATAAACTGCTGAGGAGGAAGTAACATAATATAGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATATGCGTCAAACCAGCTTACATTTTGCCACTTGTACATGATTTGTTGTGCATCCATACCATTATTTTCCGTTCTTTTTTTGTACACATATACTGATTGAACATTCCCGTTTATCATGACTCAAAGGAGCCGATCAAAAACTCTAATACAGTCAGTCTTAAGCCGACAACGAAAGAAATAAAGATCAAACTAAAAAATGTTTCCTCAGTGTTGATTCTGGAAAACTTCTTTAAAAGGCATTGATCTTAGTCAAACGACGGATCATTTATTCGACTCGAATAGTAAAATACGTAGTATATTTACATGGATAGAGATAGCAGCGCCGTTCGAATTCTGCGAATCATCAAGCAGCCCTCGCCACGCCTCTTTGGATGTTCTGAACAACCTGGACATTATTAGTTTGCGCTTTATGGGTGCGTATACACGGATGTGTATCTAAACGTATTTAATATCTACATATATATGTATGTATCCGTCGGGTTGCGCGTGGTGGTGGCTCAGGTAACAGATACTGGAACATATGTAGAGGTGGCTCTTTGTTCGAATACTGGCGGATCATAAAAATGTTAATGATCTTTTGACTGGCTACAGCGCCGATAAGAATATGTAATGCTTGTTTGAGTTATAATTGAATTTCGATGGCGCATAATATTTTATTATTTGTCTTGGACCAGCACAGCGCCGTGATTTTCATAATGATCTTACTGTTGTTCAGCCTCTCACTGTAGGTTATTTGTTTTCTGTTTGATGTTTTATTGATTTGTGAGCCGCTTCAAAGTGGCATAAACCAAACGCCGAACACACCAAATGCGGATACAAATCTCTATGAATCACTAAGCCTTAATCCCAATCCCAGCTTAATCCCAAGACCCGGGCTCGATTCTAATCGAATCCGGAGCTGACACGTTGCCAAGCGGCGATCTGGAGCGCTTCCGAAGAGAGATTGGATTGGCTGGCCCAAATCGGTGCTGACCTACCAAGTAATAATGCAGAACAAGTGTTTATGGGATGGGTAGGTATGTTGTTTATGGATACCATGGATACCCTATGGCTTATCATACGTACCATATGGCAATTGCAGAAATATCTCGATATAGAACAGTTTATTCACGTGATTGAACCTATTTGAAGTTGTGGCGATAGCAGGCGATGGTTTACACCGGTGTACCCCATTCATTGATATTTGTCACGCTCGCCGACCTGATAAGACCTAAGCTCACACTGGACTATATACGTACGTATATGAGTAATGCAAGACCTCTGAATAATATGTTAATTTCTGCACTTGATAACGGAGCACACACGGGCGAGGATTGGCGAAGGTCAGCGGTTATTACGTGACGATCGCTCGAAGTGGTGCGTTAGGTGCAATTTGTCAGGCGTCCAGTTGACGGAACGAAGTGGAAAACCAAAGTGGGAAGTACTCTATATATGTTCGCATATGGTGTAGTTGTCGTTCGTTACAGCACTACTCATTAATTCATCTGGCTGTTTCTGGAAGTGGATTCTTTGTTCGAGCACCAAGGGTGGAGTGAGCTTTGACAAGTGGAAGGCCTCTGAATTAATCGCATTGCATTGCGCAATGCGCTGCCGGAAGAAGCGAGTCACCAGTTTTCAGTTTTTCTCGCCGATTGTAATTGTGAGGCTTCAGTATTAAGCCGTGGCTTCCCCATCGCCTCCATTGAAGAGCACTCTTCATCTTCTGCCATTCAAATACGATTCTTGATTTTGGTCAGGGCCCGCGAACTCGAGTTGATTTCAATTGGATCGCCTGGAGTTCTCCGACTTATCGTGTATGGGTTCATTGTTCATATTTTAATGCCATGGCGATGGTGATCGTGCCACATGTATTGCAGTGTACACCAATTTCAAAATCAGCAAATCAGTTGGTCTTTCTGAAGCGCAGGGGTTAATGTGCGATTGGTAGATAGGTTAGAAATCTGAGAAGTTTGATGCCGCGCGACTGGAACTGCGGCCTTAACCTGATCTCAAAATAGCCGATCGTCGCAACAATGATGGGAATTAACAGGGCACCTAATTTGATGTCAGTTCCTAAAGATCTATGTATTGTGGCTTGTCGGACGGCATTACATGGCTCAGACTCGAACTGAAGGCAACGGCGACGGCGACGCGATGTCGTAATTAAAGAACCGCCAAGGGCCAGTGATGATTATGGGCTGGCTGGCTGGATGGGGTTTCTAATGGTTTACGACATGGCGTCAACCCAACCGGCAAGGCCAGGGCAATTAGCCGGAGCTCCGGGGTTGCGCCAGGCTGCAGAATTGGTTTAGGGAGTTCTGTTCTGCCCGGTTCTGGCCTAAGTTCTGGCTTTCGACTCCCCAAAGGGTTACGCGCGCCTTTGCAGACGGCGTCAGACGAACCTCTATTGATCCGGTGAAGGTATGGGTATACGTATATGTATGCTCCTCGCGAGTAGACCATCCTCCGTCTGCGGCCTTATCACGCTCTCGCCATCGCGAATTCCACTTAAAAGCCCTGCCCAGCCCGGCCAGCCTGCCTCCTACCAATTACCTTCGGGTGGACCGTGTCGCTGGCAATTCAATTAACAGCGGAATACCAGCGACTTACAACCTACGGCCGCGCGGCCATTAAACTGGATCAGTCGTAATCCCCCGCAAGCGGCGCCAAAATAAAAGAGCCCGAGGAGAGCCAGAGACTTTGGAAAATCATTACCAAGAAAAGTTCCACGGACCAACTACAAGACACGACTCCAGCCTCGATTCGGCGGATAGCCGGATAACAAGCTGCTGATTCGATCGCCGCCTGGCAACTAATTTCAATGTATTTGCATGGTAGTCTGTTTATACAACAATGGATATTTCGCGTACATTGTCAAATGCAGGCCCTTCGGGGCAAGGCGCAACTTTATTTGGGTACAATTCTCATCGACGAAACTGGAAACCAAAATGAAAGCCCAGACCCAATCTAAACCCAAACCGATTGCAGCTGCAGCGCAGCGAGGATGAAGACAGACCCATGACGTTGACGATTGCCCAAGACAATCCGGTAACAACGAGACAAGGACAATTCAGATGGTGAGGGTTTGGGAGGGGTAACAGAGAAAAAGAAACAGATGCACCGAACGACATAATAAAGAGTCTAAACCAAGACAAACATTATATAAAAGCTAACAGAAGCCTCTAGCCATCATATCATCATCATCGGCTTCATCGTGGTTGGGCCCAACAACTGCGAATTCTCAGGACCACAGTGAACCTCAAACTGGTCCCTGCTTCCCGTCGCCGTCGATTCCACTCCTCCGTAGCATCAATCCGATGGAGTAATGCGATTTTAATAGCGTTCGAATCATTGCCAAGCAGGCAAAACAAGGAACAGAACCGAACTGGAGTCGGAGTCAGGCCAAGCCGAGCCCAAATGTGCCGGAAGAAGTGCTCCATAAA'..b"AGCGGCGATCGAAGTCGGGCCCAGTCTTGAGATGGCTCCGAGATTGAATTGCTTTGATATTCTGGTGCTCGCATTTAATGCGTTCGACTGCTGGCACTAACGATAAATAATAAAACGTAAGAAACTGAACAACGCTGCTTTATCGACCAACGAAAACGGCACTGTCTGATCCCAGGCTAATGCTCAAAATATTATGCGCCATCAGTAATCCTGCTCAACAACGTACAATATTCAACCGTCAAAATAAATGGCTGACCACATGATCCATAATCTCAATCCTCACTCAAACTCAACAATCACTAATACATGAAAAAAGA\n++\n+10>44BA?;?9=;++*+*)0*)+37<B6B56.1=4055.C11AA=:/3,*=@2@3=-E-..3545<;..23*%&&*,::9?938;.0)*)0C0&',500141-1D?1,-8-1257)8-EE54<>BE1,.&(-.D3/5BG>28<1D@3*.*;@@B@;-++*%0/287:=)9<;@EH>;))33B011.&6<'18>?G=<:?-./2931=10156<>=:?G79G?26GJ34/0.6://6<7@??3+/>9;6D<,+-(0-(%49803@010,(((&'(/>6>(>,6C71;4,,/44(0)/18FB=;170,+289B:60/&%&*),*.49C8>1/-++)(-(.(-=73B38B@;/72C<0D+D9./6065?0-;>;;;<60>;24:19()*2/A<5510%%(70+/0:A.--,.1/+-04,*)**'&'/),+))3/2&)*15)*'()6*.'(.%%'*+*'.3$*+.()(&$&+0,.,,4+*.,,--/;+*$&)0/)(&(%))7.73,,05-)3.28B93424+*%-('+',+)''$&%)+)*),)*,C=:/,1-,,../)--(2).-&,)(&(1/.(*0),()%/&(*(5.*(,+..3534*,.7?0*%&*(''()&',*+/,2)-'%$(+5:79A//'7)+569,-))01)+&$'$'$)*&,'*)*-99))%)&#&&*%()&%*$'$%9<<+/*+()-(''$'(++,'+%'#+''&'$#'\n+@9cdbb051-6c56-4db9-9cd3-b2ecf215c6be\n+CCCATATCGGTACCGTTCCAGTTGCATTGCTCCGTTGCTGGACGCAGCTGCAGGCCACCCAATGCCGAGGCGGTGAGAGGAACCAGAGCAGACCAGCTGTTGCGGTCGAACTTCTCCAGCAGTCCATGGCCCCACTGCCCAGCACTGATGCAGTCGTGAATGCATGGCTGTAGTAAAGGGAGTAGTGGTGTAAATAAATCCAAATATGCACGTATGGCTGAAATCTCATATGGAAGTACATGCCGGAAGTAGGGCTGCCGAGGAAGAAGCATGAACCGGGGACACCCGTCACCATTTGTCCCGCCTGCTGGCCGCCTGCCTCTGTCCTCCGGCGTCCTGAACGGTAGCAGTGTTCTGGACGGTGGTTTCTATTGCGTTCTCCACATCCTGACTCCTGGTTTGTTCTGCGAATACTGGCGGATCGCCAAAATGTTAATGATCTTTGACGAATGGCGCCAACCAGGAATATTAATGCTTATTTGAGTTATAATTAAATTTCGATGGCGCATAATATTTTGTATTTGTCTTGGACCAACTTCCCAGCGCCATTGATTTTCGCCAATGATGTTGCTGTTGTTCGGCCTCTGTGTTATTTGTTTTCTGTTTGATGTTTATTGATTTGTGCTTCAAAGTGGCGCCAAGCAAACGCCGAACGCACCAAATGCGGATACAAATCTCTGTGAATCACTAAGCGCTAATCCAATCCCCGGTTTAAATCCCAAGACCCGGGCTCTCCGATTCTAATCGATCGGGTGACACACCCGAAGCGTCGGGAGCGCTGAAGAGAGAGATTGGATTGGCTGGCCAAATCGGTGCTTGACCTGACAAATGTCAGCGGCGTGCGAACAAGTGTTTATGGATGGTGGTATGTTTATGGACCTGTGAATACCTATGCGAACGTCGCATGCCGCTGACATTTGTTGGGTCAGCTATCTCTCGGCCTTTCCGATCACTCGCTAGTGTCTGATCTTCGATGAAACCCGAATCTGAAGTTGCTCGAGGATGGCACGAAGATTTGTATCGCATTTATTGGCATGGCGGTCTCAATCAACTCGGAAACATCAAACAACAAATAACTTGCAGAAAACCAGCAGCTAACATCGTGGCGAAAAATCACTGGCGCTATAACGGTCCCAGAACAAATAAATATTATGCGCCATCAACCAATACTCGAAACAAAACGTTACAGCTGTTCTAACAACCGTCAAAATCGTGGCCCATGATCGCAATGTGAACAAAATGATGCCGTCGAAGTTGCTGCTGGTTTATAAAGTGACAGTAACCGTAAATGTTGATGATCACCGTTCGCGGCAGCTCACTTTCAATATGTCGCCAGACCATATGTCATATTTGTTATTTATACCATAATTACAACCGCGACCGACACGTCGTACAAGGGCGGTATGTCGACTGCAACAACTCGGCATTTGTGCGTCAATGACAATACATGGCGCGGG\n++\n+&&&)&*%**%&$&)683B+%,2=-.&.**32@,,/?+022D76.3,.121,+3+.'$+-)4479C2/-/*++92))((++*-0:47-04'*'+612011/*&/'518+,<7484/5:55:*9=?D:=:,963/*,%$,-+*,-'-.02./-%-+*,1/+.*%&&$1**+66*56:.)68-)*.,7:;B5&07A5.,)-*1-EDI5.4,,*,$,$&&%$%)/331015-23=6)/,)'&)(-'/)(+)&(*241+*0,.5-)2,.2),++*./4447&(-=333+370/211>E69D=8<9?0(+2-79?0/),'+.,,.;3475.;**6243B;1B302730-0))22-1--+3.++5240)52A463*/&/(%*13=85A3/29:;0(+*/0G@=?+./+)40.'&$)')((+/3:79;2235<=8BA6/6>@27556=;;D@89<+$',1?6;6?9)8598;260+(-,4.-119+3E+*))=D:97.;/4-;0CC/+,-46=/455-8-+.ED1*402>6/2:650;68A5:-,/((%-/5245*/1+./BBG6&)+3/0.51/7G5?@?<E8:41),0;13&(-+/-15HA64HBA//,)/'+368=GF)575&/.''/(*-))7A6551>1..=26*>/=A;7?B/+::14699/:176;6?BD>>CE302:<44&+,3/--23A9,2/046<-9.21<9@B10<28***)*052782.A5,9D:;1;/0*+(@,&(-303((,4*>4321669.;0'*$%(+,,-+A2*/024348;-+,+),--/8-1&534;7>9=2519./0A761.,)33:?/(+5331+%*-%.,101/6.2277</+,0.:BA.44@2:0.(&1.56=DHC688A('&$$*)+97(3:./114-+*%%')'0)/)6:4102/88=B5-.-((',.*(&'(*+152+**(&(506+().+%)()'(+('*(,(%%()-AF785++,,%--'&)-*'()'.''+&$)-+,3B9=*6.),'(,*)64-%+**.,,,=CA69=1'0*/+3++0-,)$''))'&'$%'&0,,.268(,..,(-*55*-0,,+++*&/,+),('$9(,+(%+.534,618549@D<55812&)*0.+,$($$&(&+24+)*'(0/2-*3D:9=3B23-13AF>>3)++.1/'%'*/&,/(93:1*0*.*$#*$%$&.--+%$'&&9.+,)+'*(+,)+'%)()%(&((/(*&%)#$'*))&'(*(+&($'%&*/(-,*+1)21,224<:?.&&%*,&'-.6()-%%(%%+*-('%+)))0))),$&$(/6($%%(*('.*+$%&))+3.1'*#&'(.*''6;>96++(+*,,+/<8)7,$084'(&1.539492)-/*71.76,1)&%&()%64'*'(*)+,(--)+&*%&//++'&,*'%##$&+0.007B)%($&01E/*'%+-/11)-(*%%&$$$#%\n"

diff -r 97411db5f752 -r f383ca1c5033 test-data/long_reads_b_normalized.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/long_reads_b_normalized.fastq Tue Nov 05 05:06:18 2019 -0500

b'@@ -0,0 +1,24 @@\n+@29c296f1-2879-4ae7-afc7-55e36d5d1108\n+AACAGTCAGACAAATAATTAAGTATAGAACCAAAATAGTATCATCACTTGGAATCTAAACAACACTATCATAGAACAAGAATTGCCAGAAATAAATAAAATGAAGCAGTTGGCAACAAAATGTAACAATGAAAACAAATGTAAAATCAAAATATGGTATAATACTTAACGAAAACAAACTAAGTAGAGATAAACCTTACCCCATTGTACACCTTAAGCTATTAAAATAAAACCAATAGAACTTATGGGACATTGTACAATTAATATCAAATAATAATATCCACAGTTTGTATAATAGTATCAATCCTCAAGCCTCATCTTGTATTGCTTGTATTTGCCAAAACTAAAAACAAAATAATCCATTTGAATCACAAGATGCAAATCCAACTGCATCACCAGATTGCAGGGCATCAGCACCAATAGAGTGGAAGCATAAACTGCTGAGGAGGAAGTAACATAATATAGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATATGCGTCAAACCAGCTTACATTTTGCCACTTGTACATGATTTGTTGTGCATCCATACCATTATTTTCCGTTCTTTTTTTGTACACATATACTGATTGAACATTCCCGTTTATCATGACTCAAAGGAGCCGATCAAAAACTCTAATACAGTCAGTCTTAAGCCGACAACGAAAGAAATAAAGATCAAACTAAAAAATGTTTCCTCAGTGTTGATTCTGGAAAACTTCTTTAAAAGGCATTGATCTTAGTCAAACGACGGATCATTTATTCGACTCGAATAGTAAAATACGTAGTATATTTACATGGATAGAGATAGCAGCGCCGTTCGAATTCTGCGAATCATCAAGCAGCCCTCGCCACGCCTCTTTGGATGTTCTGAACAACCTGGACATTATTAGTTTGCGCTTTATGGGTGCGTATACACGGATGTGTATCTAAACGTATTTAATATCTACATATATATGTATGTATCCGTCGGGTTGCGCGTGGTGGTGGCTCAGGTAACAGATACTGGAACATATGTAGAGGTGGCTCTTTGTTCGAATACTGGCGGATCATAAAAATGTTAATGATCTTTTGACTGGCTACAGCGCCGATAAGAATATGTAATGCTTGTTTGAGTTATAATTGAATTTCGATGGCGCATAATATTTTATTATTTGTCTTGGACCAGCACAGCGCCGTGATTTTCATAATGATCTTACTGTTGTTCAGCCTCTCACTGTAGGTTATTTGTTTTCTGTTTGATGTTTTATTGATTTGTGAGCCGCTTCAAAGTGGCATAAACCAAACGCCGAACACACCAAATGCGGATACAAATCTCTATGAATCACTAAGCCTTAATCCCAATCCCAGCTTAATCCCAAGACCCGGGCTCGATTCTAATCGAATCCGGAGCTGACACGTTGCCAAGCGGCGATCTGGAGCGCTTCCGAAGAGAGATTGGATTGGCTGGCCCAAATCGGTGCTGACCTACCAAGTAATAATGCAGAACAAGTGTTTATGGGATGGGTAGGTATGTTGTTTATGGATACCATGGATACCCTATGGCTTATCATACGTACCATATGGCAATTGCAGAAATATCTCGATATAGAACAGTTTATTCACGTGATTGAACCTATTTGAAGTTGTGGCGATAGCAGGCGATGGTTTACACCGGTGTACCCCATTCATTGATATTTGTCACGCTCGCCGACCTGATAAGACCTAAGCTCACACTGGACTATATACGTACGTATATGAGTAATGCAAGACCTCTGAATAATATGTTAATTTCTGCACTTGATAACGGAGCACACACGGGCGAGGATTGGCGAAGGTCAGCGGTTATTACGTGACGATCGCTCGAAGTGGTGCGTTAGGTGCAATTTGTCAGGCGTCCAGTTGACGGAACGAAGTGGAAAACCAAAGTGGGAAGTACTCTATATATGTTCGCATATGGTGTAGTTGTCGTTCGTTACAGCACTACTCATTAATTCATCTGGCTGTTTCTGGAAGTGGATTCTTTGTTCGAGCACCAAGGGTGGAGTGAGCTTTGACAAGTGGAAGGCCTCTGAATTAATCGCATTGCATTGCGCAATGCGCTGCCGGAAGAAGCGAGTCACCAGTTTTCAGTTTTTCTCGCCGATTGTAATTGTGAGGCTTCAGTATTAAGCCGTGGCTTCCCCATCGCCTCCATTGAAGAGCACTCTTCATCTTCTGCCATTCAAATACGATTCTTGATTTTGGTCAGGGCCCGCGAACTCGAGTTGATTTCAATTGGATCGCCTGGAGTTCTCCGACTTATCGTGTATGGGTTCATTGTTCATATTTTAATGCCATGGCGATGGTGATCGTGCCACATGTATTGCAGTGTACACCAATTTCAAAATCAGCAAATCAGTTGGTCTTTCTGAAGCGCAGGGGTTAATGTGCGATTGGTAGATAGGTTAGAAATCTGAGAAGTTTGATGCCGCGCGACTGGAACTGCGGCCTTAACCTGATCTCAAAATAGCCGATCGTCGCAACAATGATGGGAATTAACAGGGCACCTAATTTGATGTCAGTTCCTAAAGATCTATGTATTGTGGCTTGTCGGACGGCATTACATGGCTCAGACTCGAACTGAAGGCAACGGCGACGGCGACGCGATGTCGTAATTAAAGAACCGCCAAGGGCCAGTGATGATTATGGGCTGGCTGGCTGGATGGGGTTTCTAATGGTTTACGACATGGCGTCAACCCAACCGGCAAGGCCAGGGCAATTAGCCGGAGCTCCGGGGTTGCGCCAGGCTGCAGAATTGGTTTAGGGAGTTCTGTTCTGCCCGGTTCTGGCCTAAGTTCTGGCTTTCGACTCCCCAAAGGGTTACGCGCGCCTTTGCAGACGGCGTCAGACGAACCTCTATTGATCCGGTGAAGGTATGGGTATACGTATATGTATGCTCCTCGCGAGTAGACCATCCTCCGTCTGCGGCCTTATCACGCTCTCGCCATCGCGAATTCCACTTAAAAGCCCTGCCCAGCCCGGCCAGCCTGCCTCCTACCAATTACCTTCGGGTGGACCGTGTCGCTGGCAATTCAATTAACAGCGGAATACCAGCGACTTACAACCTACGGCCGCGCGGCCATTAAACTGGATCAGTCGTAATCCCCCGCAAGCGGCGCCAAAATAAAAGAGCCCGAGGAGAGCCAGAGACTTTGGAAAATCATTACCAAGAAAAGTTCCACGGACCAACTACAAGACACGACTCCAGCCTCGATTCGGCGGATAGCCGGATAACAAGCTGCTGATTCGATCGCCGCCTGGCAACTAATTTCAATGTATTTGCATGGTAGTCTGTTTATACAACAATGGATATTTCGCGTACATTGTCAAATGCAGGCCCTTCGGGGCAAGGCGCAACTTTATTTGGGTACAATTCTCATCGACGAAACTGGAAACCAAAATGAAAGCCCAGACCCAATCTAAACCCAAACCGATTGCAGCTGCAGCGCAGCGAGGATGAAGACAGACCCATGACGTTGACGATTGCCCAAGACAATCCGGTAACAACGAGACAAGGACAATTCAGATGGTGAGGGTTTGGGAGGGGTAACAGAGAAAAAGAAACAGATGCACCGAACGACATAATAAAGAGTCTAAACCAAGACAAACATTATATAAAAGCTAACAGAAGCCTCTAGCCATCATATCATCATCATCGGCTTCATCGTGGTTGGGCCCAACAACTGCGAATTCTCAGGACCACAGTGAACCTCAAACTGGTCCCTGCTTCCCGTCGCCGTCGATTCCACTCCTCCGTAGCATCAATCCGATGGAGTAATGCGATTTTAATAGCGTTCGAATCATTGCCAAGCAGGCAAAACAAGGAACAGAACCGAACTGGAGTCGGAGTCAGGCCAAGCCGAGCCCAAATGTGCCGGAAGAAGTGCTCCATAAA'..b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diff -r 97411db5f752 -r f383ca1c5033 update_mapq.xml
--- a/update_mapq.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/update_mapq.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.16">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.17">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[

diff -r 97411db5f752 -r f383ca1c5033 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml Thu Sep 05 10:22:27 2019 -0400
+++ b/write_supplementary_fastq.xml Tue Nov 05 05:06:18 2019 -0500

[

@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.16">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.17">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[