# HG changeset patch
# User mvdbeek
# Date 1564333148 14400
# Node ID 7191da0bc7be7b322df56bfbe0a4d716872667d7
# Parent  5eb0ec276ea5fc8690abcc3299462508f6823d4e
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920

diff -r 5eb0ec276ea5 -r 7191da0bc7be add_matesequence.xml
--- a/add_matesequence.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/add_matesequence.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.1">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.2">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5eb0ec276ea5 -r 7191da0bc7be all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Sun Jul 28 12:59:08 2019 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 5eb0ec276ea5 -r 7191da0bc7be allow_dovetailing.xml
--- a/allow_dovetailing.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/allow_dovetailing.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.1">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.2">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 5eb0ec276ea5 -r 7191da0bc7be bam_readtagger.xml
--- a/bam_readtagger.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/bam_readtagger.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.1">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.2">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 5eb0ec276ea5 -r 7191da0bc7be extract_variants.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_variants.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -0,0 +1,37 @@
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.1">
+    <description>from long reads</description>
+    <requirements>
+        <requirement type="package" version="0.5.1">readtagger</requirement>
+    </requirements>
+    <version_command>extract_variants --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+ln -fs '$insert_reference.fields.path' reference.fa &&
+extract_variants '$input' '$output' reference.fa
+    ]]></command>
+    <inputs>
+        <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
+        <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select">
+            <options from_data_table="all_fasta"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input"/>
+    </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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Extract variants will find soft-clipped alignments and alignments with insertions,
+and, if the inserted sequence aligns with the selected reference, write out
+a the alignment, but clip the aligned portion of the read to a single N
+and will add 2 tags, AR and AD to the alignment.
+The AR tag will list the contig, the AD tag contains detailed
+information on how the insert/clipped sequence aligned against the selected
+reference.
+    ]]></help>
+</tool>
diff -r 5eb0ec276ea5 -r 7191da0bc7be filter_insertions.xml
--- a/filter_insertions.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/filter_insertions.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.1">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.2">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5eb0ec276ea5 -r 7191da0bc7be findcluster.xml
--- a/findcluster.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/findcluster.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.1">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.2">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5eb0ec276ea5 -r 7191da0bc7be plot_coverage.xml
--- a/plot_coverage.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/plot_coverage.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.1">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.2">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Sun Jul 28 12:59:08 2019 -0400
@@ -0,0 +1,1 @@
+transposon	transposon	transposon	${__HERE__}/transposon.fa
diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/long_insert_tagged.bam
Binary file test-data/long_insert_tagged.bam has changed
diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/long_insertion.bam
Binary file test-data/long_insertion.bam has changed
diff -r 5eb0ec276ea5 -r 7191da0bc7be test-data/transposon.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transposon.fa	Sun Jul 28 12:59:08 2019 -0400
@@ -0,0 +1,80 @@
+>F-element
+AATCAATTAATCAATTCGATCGCCGACGTGTGAAGACGTTTTTATCGTGCTCCGCACAAA
+ATCGGTTGTTTTGAGTGAAGTGAACGCCAAATAAAATAAACTAAATAAAAAATCTGAAAG
+CGAAAGAGACGCTCTATGCGATGCAAGATCGCTTAAATACATAGTGAATTGTTATCTTAA
+ATAATAAAACTATGAGTCAGAATGACACTCGCGCCCAGCGTCAGCGCGAGCATGACGAAC
+GCCGACTCTCAATTCAGCGCAACAACGCGTACTTCTCCTACGTCTCACCGACAATCCCAA
+ACGCAGACATCGAGCGGTCAATAACCCATAGCCCAGGAAACCTTCTTCTACCAACAAATC
+AAGAAAGAGCGCGCTCCTGCTCTCCCGCTCTATTGGCTCCGACAGAAGCCCCGCTACCTC
+CAACAACAACAGCTGGAGAGGGACCGGCAGCCCGCTCTGCCTCGTCATCGGCTGCACCCG
+CTCACGGTCTGACTAAGTCAGCGAAAGCAAAACCGCTAGCAATAAACGGTACTGCTGCAC
+TGCCAGCAAAACAAAACGAAAACGTAAACAAAAAAGCTGGGTCGACCTGGCAGACTGGAA
+TGGACCGCTACATTACAATAAAGCGAAAGCTCAGCCCGGAAAATTCAGATTTGGGAAACA
+AGCCGAAAAATACACGCGATAACTCTACCTTGATCAAAAATGTAGCCCCTGCAAATACCA
+ACAGATTTGCCTTGCTGGTAGATACCGCTGAGGACGTGCCGCTGGGATCCGTTGATATCG
+AACCGAAGAAAACAAAGCCTCCGCCAATATACATCCGCGAGAAGAGCACAAGCCGTCTTG
+TAAATACTTTGATTGGCCTTATTGGGAAAGATAGCTTTCATATAATTCCCCTCGTAAGAG
+GTACTATCAACGAAATCAAACTTCAGACGAAAACGGAGGACGACTACAGAAAAGTCACAA
+ACTATTTTACCGCACAAAAAATAGGCTTCTACACCTACCAGCTTAAAAGCAGCAAGGGCC
+TGCAAGTAGTCCTGAAGGGCATTGAGTCTGATGTTACGCCCGAAGAGATAACTGAGGCGC
+TAAAGGAAAAGGGATTTTACGCCAAAAACGTGTTCAATATCAAAAACAGAAACAGGCAGC
+CCCAACCACTCTTCAAGATTGAGCTTGAACCAGAAAACAAGCCTCCTAGAAAAAACGAGG
+TTCACCCAATTTACAAACTCCAGCTCCTTTTGCACCGTAGGATCACGGTAGAAGAGCCGC
+ACAAACGCAACGCTCCTGTACAATGTACAAACTGCCAAGAGTATGGCCACACGAGGTCAT
+ATTGTACACTTCGCCCGGTGTGCGTAGTCTGTGGAGATCTCCACGACTCCAAACAGTGTC
+AAATTAACAAAGAAAATGCATGCGAGAAAAAATGTAATAACTGCGGGGGCAATCACACAG
+CAAACTACAGAGGCTGTCCAATCTACAAAGAGCTGAAAATCCGTCTTCACAAAAGAATGA
+ACACGGCGCGGGCACACCAAGGATCAGCTACCCTGATACCATCAGAGACAAATCCTGAAG
+TAATTTTCTCGAAAGCAGCTAGTTTCGCTCCCTGGCCTACATTCAACACTAACAAGACAA
+CATTTGCTAACGTTTTAAAATCAGGTATGACGCCTCCAACCCAAAACTCCCGAACTCCAC
+ATGAAGTGCACACAAAATTAGACACACAACAAAACTATCACCCAGCTGCGCAGCAGGAAA
+CAAAAACTGAAGCTATGATGCAAGCCTTACAACAGAGCATGATGGAATTTATGACATTTA
+TGAAGACCACCATTCAAGACATGATGCGTAATCAAAACCTTTTGATACAAATGCTTGTAG
+CCCAACAATCAAATAAATAATGGCTACCTTACGCATAGCTACGTGGAACGCCAATGGCGT
+CTCACAGCGCAAACTTGAGCTAGCTCAATTCCTACATGAGAAGCATATCGACGTAATGCT
+TCTTTCGGAAACTCATCTCACAAGCAAATACAATTTTCAAATAAGAGACTACCATTTCTA
+CGGTACAAATCATCCCGACGGAAAAGCACACGGTGGCACCGCCATACTCATAAGGAACCG
+TATGAAGCACCACTTTTACAAAGAATTTGCGGAAAATCATCTTCAGGCCACATCTATCAA
+CATTCAGCTGGATGACAACACTCTCCTTACACTAGCGGCCGTATACTGCCCCCCCCGTTT
+CACAGTATTAGAAGCTCAATTCCTGGATTTCTTCCAAGCACTAGGGCCACACTTCATTGC
+AGCAGGCGACTACAACGCTAAACATACTCACTGGGGATCGCGACTTGTGAACCCAAAAGG
+AAAACAGCTTTATAAGACGATAATAAAAGCCACTAATAAACTTGACCATGTTTCCCCCGG
+GAGTCCTACATACTGGCCATCAGACCTCAATAAGCTGCCAGACCTGATCGACTTCGCAGT
+TACGAAAAATATTTCCCGCAGTTTGGTTAAAGCTGAATGTCTGCCGGATCTCTCATCTGA
+TCACTCGCCTGTACTAATTCACCTCCGCCGATACGCAGAAAACGTGAAACCACCAACCAG
+ATTGACCTCTAGCAAAACAAACTGGCTCAGGTATAAAAAATATATAAGTTCACATATTGA
+GCTAAGCCCAAAACTCAATACTGAATCTGATATAGAGAGCTGCACGTGTGCATTGCAATC
+CATCCTTACTGCAGCAGCTCTTACTGCAACACCCAAAATAACAAATAATACAATTAATTC
+AAAAAAGACCAACGTACAAATCGAGCAACTCGTCCACGTAAAACGTCGCTTACGCAGAGA
+ATGGCAATCTTCCAGATCCCCAACTGCAAAACAAAAGCTAAAAGTAGCCACACGGAAACT
+GGCCAACGCTCTGAAACAAGAAGAGGACGACGATCAGCGCCGATACATAGAGCAACTCAC
+ACCAACAGGCACAAAACAAAAGTCACTGTGGCGAGCCCACTCAACTCTTCGCCCACCGAC
+TGAAACCGTTTTGCCGATAAGGAATTCATCAGGTGGCTGGGCCCGTAGTGATGAAGACAG
+AGCCAACACATTTGCCGCTCACCTACAAAATGTGTTCACGCCAAACCAGGCTACTAGCAC
+ATTCGCGCTACCGTCCTATCCCGTAAACCGCCATCAGCAACACACCCCAATTGTGTTTCG
+TCCTAAAGAAATAACTAAAATAATCAAAGACAATCTCAGCCCGAAAAAATCCCCCGGCTA
+CGACCTTATAACACCGGAAATGATCATCCAGCTGCCACATTCTGCAGTTCGCTACATAAC
+CAAGCTCTTTAATGCCATCACCAAACTTGGTTACTTTCCACAACGATGGAAGATGATGAA
+GATCATAATGATTCCAAAGCCTGGTAAGAACCACACAGTCGCTTCATCTTACAGACCAAT
+AAGTCTACTCTCATGCATTTCGAAACTATTCGAAAAATGCCTGCTGATCCGACTTAATCA
+ACATCTGATATACCACAATATAATCCCAGCCCACCAATTTGGATTTCGCGAAAGCCACGG
+AACCATTGAACAGGTGAATCGTATTACAACGGAAATAAGAACTGCATTTGAATATCGCGA
+ATACTGTACAGCAGTATTTTTAGACGTATCCCAAGCATTCGACAAAGTCTGGCTCGACGG
+CCTAATGTTTAAAATTAAAACATCCCTACCCGAAAGCACACACAAACTTCTAAAGTCTTA
+CCTCTATGACAGAAAGTTTGCAGTGCGGTGCAACACTGCCACTTCCACTGTTCATACAAT
+TGAGGCTGGAGTCCCCCAAGGCAGCGTTCTTGGGCCAACCTTATACCTCATCTATACAGC
+CGACATCCCTACAAATAGTCGCTTAACGGTATCCACATTTGCCGACGATACAGCTATCCT
+TAGCCGTTCAAGGTCCCCTATCCAAGCTACAGCACAGTTGGCACTGTACCTCATCGACAT
+TGAGAAGTGGCTCTCTGACTGGCGAATAAAAGTAAACGAGCAAAAATGCAAGCACGTGAC
+GTTTACGCTAAACAGACAAGACTGTCCTCCGCTCTTGTTGAACAGCATACCACTCCCGAA
+AGCAGACGAGGTAACGTACCTAGGAGTACACCTAGACAGAAGACTCACATGGCGCAGGCA
+CATTGAAGCCAAAAAAACCCAACTTAAACTCAAAGCCAACAACTTACACTGGCTCATCAA
+CTCTGGTTCTCCGCTCAGCCTAGATCACAAGGTCTTGCTCTACAATTCTATATTGAAACC
+AATCTGGACCTATGGCTCACAGTTATGGGGCAATGCCAGCAACAGCAATATTGACATCAT
+TCAGCGAGCACAATCAAAGATTCTGAGAACCATCACTGGGGCACCGTGGTACGTTCGGAG
+TGAAAACATCCAAAGAGACTTAAATATCCCATCAGTTACCAACGCAATCACGGAACTTAA
+GGAAAAATACCATAGCAAGCTTCACACGCACCCCAACCACCTAGCGCGAGGTCTAATCCA
+GCTCAGCAGCCGTTCCCGTCTCCGGCGAAAGGACCTACCAACCCAGCGAATAAATTATTA
+GGGCCGTTTAAACATAGAACAGTTGGAAAAATAATACAACTGTTCAAAAAATACTTGTTA
+TAGTTAAGATTTTTAAACTTATTGTTAGTTCTTATACAAGAAGATTCAATAAATAAAAGC
+AAAGTAAAATAAAAAAAAAAAAAAAAAA
diff -r 5eb0ec276ea5 -r 7191da0bc7be tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Jun 13 12:52:17 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Sun Jul 28 12:59:08 2019 -0400
@@ -5,4 +5,9 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bwa_mem_index.loc" />
     </table>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
 </tables>
diff -r 5eb0ec276ea5 -r 7191da0bc7be tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Sun Jul 28 12:59:08 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 5eb0ec276ea5 -r 7191da0bc7be update_mapq.xml
--- a/update_mapq.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/update_mapq.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.1">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.2">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5eb0ec276ea5 -r 7191da0bc7be write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Thu Jun 13 12:52:17 2019 -0400
+++ b/write_supplementary_fastq.xml	Sun Jul 28 12:59:08 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.1">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.2">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.1">readtagger</requirement>
+        <requirement type="package" version="0.5.2">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[