# HG changeset patch
# User mvdbeek
# Date 1488968065 18000
# Node ID 53b71263e2a2fa38b375a78ef7b7aea0846793ac
# Parent  bf8ffb337cbef98969404cc507b38ff4697a3ec0
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty

diff -r bf8ffb337cbe -r 53b71263e2a2 add_matesequence.xml
--- a/add_matesequence.xml	Sun Mar 05 13:29:42 2017 -0500
+++ b/add_matesequence.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.4">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.5">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.4">readtagger</requirement>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r bf8ffb337cbe -r 53b71263e2a2 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Mar 05 13:29:42 2017 -0500
+++ b/allow_dovetailing.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.4">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.5">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.4">readtagger</requirement>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r bf8ffb337cbe -r 53b71263e2a2 bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Mar 05 13:29:42 2017 -0500
+++ b/bam_readtagger.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.4">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.5">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.4">readtagger</requirement>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
diff -r bf8ffb337cbe -r 53b71263e2a2 findcluster.xml
--- a/findcluster.xml	Sun Mar 05 13:29:42 2017 -0500
+++ b/findcluster.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.4">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.5">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.4">readtagger</requirement>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/remapped_supplementary.bam
Binary file test-data/remapped_supplementary.bam has changed
diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary.bam
Binary file test-data/supplementary.bam has changed
diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/supplementary.fastq	Wed Mar 08 05:14:25 2017 -0500
@@ -0,0 +1,36 @@
+@HWI-D00405:129:C6KNAANXX:3:2115:7866:72488
+AAAGAAATAATTAGTTTTCCGCTCTTTTTATGTAAAATCGT
++
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@HWI-D00405:129:C6KNAANXX:3:2210:21010:12528
+AAGAAATAATTAGTTTTCCGCTCTTTTTATGTAAAATCGT
++
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@HWI-D00405:129:C6KNAANXX:3:1312:14525:13985
+AATTAGTTTTCCGCTCTTTTTATGTAAAATCGT
++
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@HWI-D00405:129:C6KNAANXX:3:2112:20719:46788
+ATTAGTTTTCCGCTCTTTTTATGTAAAATCGT
++
+BBBBBFFFFBFFFFFFFFFFBFFFFFFFFFFF
+@HWI-D00405:129:C6KNAANXX:4:1112:20453:89309
+ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCAT
++
+FFFFFFFFFBFBBFFFFFFFFFBBF/BFFF<FB<</F<F
+@HWI-D00405:129:C6KNAANXX:4:2201:13501:43210
+ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTGAT
++
+BFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<BFFFFFBFFFFFFBFBF
+@HWI-D00405:129:C6KNAANXX:3:1210:5442:13792
+ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCAT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@HWI-D00405:129:C6KNAANXX:4:1112:20453:89309
+ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTG
++
+FFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB
+@HWI-D00405:129:C6KNAANXX:3:1210:5442:13792
+ATCGTATTATTGAATGTTATTACGTGCTAGGGCGATCATTTGTGCTAGTG
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB
diff -r bf8ffb337cbe -r 53b71263e2a2 test-data/supplementary_new_mapq.bam
Binary file test-data/supplementary_new_mapq.bam has changed
diff -r bf8ffb337cbe -r 53b71263e2a2 update_mapq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update_mapq.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -0,0 +1,45 @@
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.5">
+    <description>of supplementary alignments</description>
+    <requirements>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
+    </requirements>
+    <version_command>update_mapq --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
+    ]]></command>
+    <inputs>
+        <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
+        <param argument="--remapped_path" label="Extarct MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
+    </inputs>
+    <outputs>
+        <data name="output_path" format="bam"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source_path" value="supplementary.bam" ftype="bam"/>
+            <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
+            <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. code-block::
+
+    Usage: update_mapq [OPTIONS]
+
+      Update supplementary read MAPQ score after remapping.
+
+    Options:
+      --source_path PATH    Alignment file where supplementary reads should be
+                            updated with new MAPQ scores  [required]
+      --remapped_path PATH  Alignment file that contains reads that have been
+                            remapped and contain an updated MAPQ score  [required]
+      --output_path PATH    Write all alignments in original_path to this
+                            location. Supplementary reads will take the MAPQ score
+                            as determined by remapping to the alignment file at
+                            `remapped_path`  [required]
+      --version             Show the version and exit.
+      --help                Show this message and exit.
+
+
+    ]]></help>
+</tool>
diff -r bf8ffb337cbe -r 53b71263e2a2 write_supplementary_fastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/write_supplementary_fastq.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -0,0 +1,37 @@
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.5">
+    <description>from SAM/BAM alignment files as FASTQ</description>
+    <requirements>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
+    </requirements>
+    <version_command>write_supplementary_fastq --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        write_supplementary_fastq --input_path '$input' --output_path '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" argument="--input_path" type="data" format="bam"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fastqsanger"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="supplementary.bam" ftype="bam"/>
+            <output name="output" file="supplementary.fastq" ftype="fastqsanger"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. code-block::
+
+    Usage: write_supplementary_fastq [OPTIONS]
+
+      Write all supplementary alignments in `input_path` to an output fastq file
+      at `output_path`.
+
+    Options:
+      --input_path PATH   Collect supplementary reads in this alignment file.
+      --output_path PATH  Write supplementary reads to this FASTQ file.
+      --help              Show this message and exit.
+
+
+    ]]></help>
+</tool>