| Previous changeset 19:97c1b92dbd28 (2017-04-05) Next changeset 21:1c91108a80d5 (2017-04-20) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml update_mapq.xml write_supplementary_fastq.xml |
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| diff -r 97c1b92dbd28 -r 03415763c62c add_matesequence.xml --- a/add_matesequence.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/add_matesequence.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.13"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.14"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 97c1b92dbd28 -r 03415763c62c allow_dovetailing.xml --- a/allow_dovetailing.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/allow_dovetailing.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.13"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.14"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' @@ -15,7 +15,7 @@ <tests> <test> <param name="input" value="not_a_proper_pair.bam" ftype="bam"/> - <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help><![CDATA[ |
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| diff -r 97c1b92dbd28 -r 03415763c62c bam_readtagger.xml --- a/bam_readtagger.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/bam_readtagger.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.14"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a @@ -54,9 +54,9 @@ </repeat> <param name="discarded" value="True"/> <param name="verified" value="True"/> - <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/> - <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/> - <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/> + <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/> + <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/> + <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/> </test> <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) --> <param name="tag_file" value="pasteurianus.bam" ftype="bam"/> @@ -67,9 +67,9 @@ </repeat> <param name="discarded" value="True"/> <param name="verified" value="True"/> - <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" /> - <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/> - <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/> + <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" /> + <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/> + <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/> </test> <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair --> <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/> @@ -82,9 +82,9 @@ <param name="keep_suboptimal" value="True"/> <param name="discard_proper_pairs" value="True"/> <param name="verified" value="True"/> - <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" /> - <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/> - <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/> + <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" /> + <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/> + <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/> </test> </tests> <help><![CDATA[ |
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| diff -r 97c1b92dbd28 -r 03415763c62c findcluster.xml --- a/findcluster.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/findcluster.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.13"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.14"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 97c1b92dbd28 -r 03415763c62c update_mapq.xml --- a/update_mapq.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/update_mapq.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.13"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.14"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r 97c1b92dbd28 -r 03415763c62c write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Wed Apr 05 17:34:55 2017 -0400 +++ b/write_supplementary_fastq.xml Wed Apr 19 16:23:12 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.13"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.14"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.13">readtagger</requirement> + <requirement type="package" version="0.3.14">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |