Mercurial > repos > mvdbeek > bam_readtagger

changeset 78:6178c24ddd5a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
author mvdbeek
date Tue, 07 Apr 2020 08:57:47 -0400
parents b9b76f9a816c
children c42dd2551c9c
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml test-data/three_cluster_plot.pdf test-data/three_cluster_plot_line.pdf update_mapq.xml write_supplementary_fastq.xml
diffstat 12 files changed, 34 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/add_matesequence.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.23">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.24">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/allow_dovetailing.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.23">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.24">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/bam_readtagger.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.23">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.24">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
--- a/extract_variants.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/extract_variants.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.23">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.24">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/filter_insertions.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.23">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.24">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/findcluster.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.23">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.24">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/normalize_readsizes.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/normalize_readsizes.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.23">
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.24">
     <description>of multiple fastq files</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>normalize_readsizes --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/plot_coverage.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.23">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.24">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 #import re
@@ -10,7 +10,7 @@
     #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
     --file '$r.input' '$identifier' $r.total_reads
 #end for
-output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
+output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind
     ]]></command>
     <inputs>
         <repeat name="input_files" title="Add input files to coverage plot" min="1">
@@ -27,6 +27,10 @@
                 </valid>
             </sanitizer>
         </param>
+        <param name="plot_kind" type="select" label="Select the plot type">
+            <option value="area">Area plot</option>
+            <option value="line">Line plot</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
@@ -40,6 +44,15 @@
             <param name="regions" value="3R:13373525-13373615"/>
             <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
+            <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
+            <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
+            <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
+            <param name="regions" value="3R:13373525-13373615"/>
+            <param name="plot_kind" value="line"/>
+            <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 
Binary file test-data/three_cluster_plot.pdf has changed
Binary file test-data/three_cluster_plot_line.pdf has changed
--- a/update_mapq.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/update_mapq.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.23">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.24">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/write_supplementary_fastq.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.23">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.24">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[