Mercurial > repos > mvdbeek > bam_readtagger
changeset 42:fbfd1082de71 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c
author | mvdbeek |
---|---|
date | Fri, 26 Oct 2018 06:10:14 -0400 |
parents | 29734dbad6de |
children | c2104094afd3 |
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, 39 insertions(+), 35 deletions(-) [+] |
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--- a/add_matesequence.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/add_matesequence.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.10"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.12"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/allow_dovetailing.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.10"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.12"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/bam_readtagger.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,31 +1,31 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - readtagger -t '$tag_file' -s - #for $element in $alignment_series - '$element.annotate_with':$element.r_tag:$element.m_tag - #end for - #if $reference_fasta: - --reference_fasta '$reference_fasta' - #end if - $allow_dovetailing - $discard_suboptimal - $discarded - $verified - $discard_proper_pairs - --cores "\${GALAXY_SLOTS:-2}" - -o '$tagged_file' +readtagger -t '$tag_file' -s +#for $element in $alignment_series + '$element.annotate_with':$element.r_tag:$element.m_tag +#end for +#if $reference_fasta: + --reference_fasta '$reference_fasta' +#end if +$allow_dovetailing +$discard_suboptimal +$discarded +$verified +$discard_proper_pairs +--cores "\${GALAXY_SLOTS:-2}" +-o '$tagged_file' ]]></command> <inputs> - <param name="tag_file" argument="--tag_file" type="data" format="bam"/> + <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/> <repeat name="alignment_series" title="Alignments"> - <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> + <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,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 Apr 01 03:38:16 2018 -0400 +++ b/filter_insertions.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,24 +1,28 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.12"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ ln -fs $putative_insertions putative_insertions.gff && ln -fs $all_insertions all_insertions.gff && - ln -fs $all_controls all_controls_path.gff && + #for i, p in enumerate($all_controls) + ln -fs '$p' all_controls_${i}.gff && + #end for confirm_insertions --putative_insertions_path putative_insertions.gff --all_treatments_path all_insertions.gff - --all_controls_path all_controls_path.gff + #for i, p in enumerate($all_controls) + --all_controls_paths all_controls_${i}.gff + #end for --output_path '$output' $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 control sample" argument="--all_controls_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="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 Apr 01 03:38:16 2018 -0400 +++ b/findcluster.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.10"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.12"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/plot_coverage.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/plot_coverage.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.4.10"> +<tool id="plot_coverage" name="Plot coverage" version="0.4.12"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re
--- a/update_mapq.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/update_mapq.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.10"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.12"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml Sun Apr 01 03:38:16 2018 -0400 +++ b/write_supplementary_fastq.xml Fri Oct 26 06:10:14 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.10"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.12"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.10">readtagger</requirement> + <requirement type="package" version="0.4.12">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[