Mercurial > repos > mvdbeek > bam_readtagger

changeset 79:c42dd2551c9c draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
author mvdbeek
date Tue, 07 Apr 2020 13:41:14 -0400
parents 6178c24ddd5a
children c9361b7a025d
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml update_mapq.xml write_supplementary_fastq.xml
diffstat 10 files changed, 44 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/add_matesequence.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.24">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.25">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/allow_dovetailing.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.24">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.25">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/bam_readtagger.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.24">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.25">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
--- a/extract_variants.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/extract_variants.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.24">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.25">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/filter_insertions.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.24">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.25">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/findcluster.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.24">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.25">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/normalize_readsizes.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/normalize_readsizes.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.24">
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.25">
     <description>of multiple fastq files</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>normalize_readsizes --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/plot_coverage.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.24">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.25">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">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' --plot_kind $plot_kind
+output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind --style $style
     ]]></command>
     <inputs>
         <repeat name="input_files" title="Add input files to coverage plot" min="1">
@@ -31,6 +31,29 @@
             <option value="area">Area plot</option>
             <option value="line">Line plot</option>
         </param>
+       <param name="style" type="select" label="Select a plotting style">
+           <option value="ggplot">ggplot</option>
+           <option value="classic">classic</option>
+           <option value="greyscale">greyscale</option>
+           <option value="dark_background">dark_background</option>
+           <option value="seaborn">seaborn</option>
+           <option value="seaborn-bright">seaborn-bright</option>
+           <option value="seaborn-colorblind">seaborn-colorblind</option>
+           <option value="seaborn-dark">seaborn-dark</option>
+           <option value="seaborn-dark-palette">seaborn-dark-palette</option>
+           <option value="seaborn-darkgrid">seaborn-darkgrid</option>
+           <option value="seaborn-deep">seaborn-deep</option>
+           <option value="seaborn-muted">seaborn-muted</option>
+           <option value="seaborn-notebook">seaborn-notebook</option>
+           <option value="seaborn-paper">seaborn-paper</option>
+           <option value="seaborn-pastel">seaborn-pastel</option>
+           <option value="seaborn-poster">seaborn-poster</option>
+           <option value="seaborn-talk">seaborn-talk</option>
+           <option value="seaborn-ticks">seaborn-ticks</option>
+           <option value="seaborn-white">seaborn-white</option>
+           <option value="seaborn-whitegrid">seaborn-whitegrid</option>
+           <option value="tableau-colorblind10">tableau-colorblind10</option>
+       </param>
     </inputs>
     <outputs>
         <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
--- a/update_mapq.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/update_mapq.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.24">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.25">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml	Tue Apr 07 08:57:47 2020 -0400
+++ b/write_supplementary_fastq.xml	Tue Apr 07 13:41:14 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.24">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.25">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.24">readtagger</requirement>
+        <requirement type="package" version="0.5.25">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[