| Previous changeset 32:bf3d04937095 (2017-06-21) Next changeset 34:240c901dedc0 (2017-11-20) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh findcluster.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r bf3d04937095 -r c7f140920cc1 add_matesequence.xml --- a/add_matesequence.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/add_matesequence.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.25"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.0"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r bf3d04937095 -r c7f140920cc1 allow_dovetailing.xml --- a/allow_dovetailing.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/allow_dovetailing.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.25"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.0"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r bf3d04937095 -r c7f140920cc1 bam_readtagger.xml --- a/bam_readtagger.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/bam_readtagger.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.25"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.0"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r bf3d04937095 -r c7f140920cc1 findcluster.xml --- a/findcluster.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/findcluster.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.25"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.0"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -16,14 +16,14 @@ #if str($transposon_source.reference_source_selector) == "history": --transposon_reference_fasta '$transposon_source.ref_file' #else : - --transposon_bwa_index '$transposon_source.ref_file.fields.path' + --transposon_bwa_index '$reference_source.ref_file.fields.path' #end if #end if #if $genome_source.ref_file: #if str($genome_source.reference_source_selector) == "history": --genome_reference_fasta '$genome_source.ref_file' #else : - --genome_bwa_index '$genome_source.ref_file.fields.path' + --genome_bwa_index '$reference_source.ref_file.fields.path' #end if #end if --output_bam '$output_bam' |
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| diff -r bf3d04937095 -r c7f140920cc1 update_mapq.xml --- a/update_mapq.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/update_mapq.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.25"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.0"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r bf3d04937095 -r c7f140920cc1 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Wed Jun 21 09:57:48 2017 -0400 +++ b/write_supplementary_fastq.xml Thu Nov 09 06:49:15 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.25"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.0"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.25">readtagger</requirement> + <requirement type="package" version="0.4.0">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |