Mercurial > repos > mvdbeek > bam_readtagger
changeset 48:54aafdb84833 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054
author | mvdbeek |
---|---|
date | Wed, 12 Jun 2019 14:23:18 -0400 |
parents | 21acaf15af89 |
children | 534d6b4aebb0 |
files | add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/extended_and_annotated_roi.bam.bai test-data/out.png test-data/three_cluster_out.bam.bai update_mapq.xml write_supplementary_fastq.xml |
diffstat | 11 files changed, 21 insertions(+), 21 deletions(-) [+] |
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--- a/add_matesequence.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/add_matesequence.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.17"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.0"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/allow_dovetailing.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.17"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.0"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/bam_readtagger.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.17"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.0"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s @@ -23,9 +23,9 @@ -o '$tagged_file' ]]></command> <inputs> - <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_input_sorted.bam"/> + <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_sorted.bam"/> <repeat name="alignment_series" title="Alignments"> - <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_input_sorted.bam"/> + <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_sorted.bam"/> <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> <expand macro="tag_options"/> </param>
--- a/filter_insertions.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/filter_insertions.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.17"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.0"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -20,9 +20,9 @@ $output_discard ]]></command> <inputs> - <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> - <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> - <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> + <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/> + <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> + <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> </inputs> <outputs>
--- a/findcluster.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/findcluster.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.17"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.0"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/plot_coverage.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.17"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.0"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re
--- a/update_mapq.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/update_mapq.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.17"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.0"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml Sun Feb 10 15:58:36 2019 -0500 +++ b/write_supplementary_fastq.xml Wed Jun 12 14:23:18 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.17"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.0"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.17">readtagger</requirement> + <requirement type="package" version="0.5.0">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[