Mercurial > repos > mvdbeek > bam_readtagger
changeset 65:08a10eefc2ca draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
| author | mvdbeek |
|---|---|
| date | Tue, 05 Nov 2019 05:05:32 -0500 |
| parents | 31dc40ec7067 |
| children | 9ac536101591 |
| files | add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml normalize_readsizes.xml plot_coverage.xml test-data/long_insert_tagged.tab test-data/long_reads_a.fastq test-data/long_reads_a_normalized.fastq test-data/long_reads_b.fastq test-data/long_reads_b_normalized.fastq update_mapq.xml write_supplementary_fastq.xml |
| diffstat | 15 files changed, 167 insertions(+), 21 deletions(-) [+] |
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--- a/add_matesequence.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/add_matesequence.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.16"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.17"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/allow_dovetailing.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.16"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.17"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/bam_readtagger.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.16"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.17"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s
--- a/extract_variants.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/extract_variants.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,12 +1,13 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.16"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.17"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ ln -fs '$insert_reference.fields.path' reference.fa && -extract_variants '$input' '$output' reference.fa +extract_variants '$input' '$output_alignment' reference.fa && +summarize_fragments '$output_alignment' '$output_tabular' ]]></command> <inputs> <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> @@ -15,13 +16,15 @@ </param> </inputs> <outputs> - <data name="output" format_source="input"/> + <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/> + <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/> </outputs> <tests> <test> <param name="input" value="long_insertion.bam" ftype="bam"/> <param name="insert_reference" value="transposon"/> - <output name="output" file="long_insert_tagged.bam" ftype="bam"/> + <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/> + <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/> </test> </tests> <help><![CDATA[
--- a/filter_insertions.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/filter_insertions.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.16"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.17"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/findcluster.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/findcluster.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.16"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.17"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalize_readsizes.xml Tue Nov 05 05:05:32 2019 -0500 @@ -0,0 +1,45 @@ +<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17"> + <description>of multiple fastq files</description> + <requirements> + <requirement type="package" version="0.5.17">readtagger</requirement> + </requirements> + <version_command>normalize_readsizes --version</version_command> + <command detect_errors="aggressive"><![CDATA[ +#for $i, $element in enumerate($input): + ln -fs '$element' '${i}.${element.ext}' && +#end for +normalize_readsizes +#for $i, $element in enumerate($input): + -i '${i}.${element.ext}' + -o '${i}.out.${element.ext}' +#end for +#for $i, $element in enumerate($output): + && mv '${i}.out.${element.ext}' '$element' +#end for + ]]></command> + <inputs> + <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/> + </inputs> + <outputs> + <collection name="output" type="list" structured_like="input" inherit_format="true"/> + </outputs> + <tests> + <test> + <param name="input"> + <collection type="list"> + <element name="a" value="long_reads_a.fastq" /> + <element name="b" value="long_reads_b.fastq" /> + </collection> + </param> + <param name="insert_reference" value="transposon"/> + <output_collection name="output"> + <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/> + <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same +across all datasets. + ]]></help> +</tool>
--- a/plot_coverage.xml Thu Sep 05 10:21:59 2019 -0400 +++ b/plot_coverage.xml Tue Nov 05 05:05:32 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.16"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.17"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.16">readtagger</requirement> + <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <command detect_errors="aggressive"><