| Previous changeset 7:d2009cdcdeba (2017-03-03) Next changeset 9:53b71263e2a2 (2017-03-08) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml test-data/three_cluster_out.bam test-data/three_cluster_out.gff |
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| diff -r d2009cdcdeba -r bf8ffb337cbe add_matesequence.xml --- a/add_matesequence.xml Fri Mar 03 10:30:14 2017 -0500 +++ b/add_matesequence.xml Sun Mar 05 13:29:42 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.3"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.4"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.3">readtagger</requirement> + <requirement type="package" version="0.3.4">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r d2009cdcdeba -r bf8ffb337cbe allow_dovetailing.xml --- a/allow_dovetailing.xml Fri Mar 03 10:30:14 2017 -0500 +++ b/allow_dovetailing.xml Sun Mar 05 13:29:42 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.3"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.4"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.3">readtagger</requirement> + <requirement type="package" version="0.3.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r d2009cdcdeba -r bf8ffb337cbe bam_readtagger.xml --- a/bam_readtagger.xml Fri Mar 03 10:30:14 2017 -0500 +++ b/bam_readtagger.xml Sun Mar 05 13:29:42 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.3"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.4"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.3">readtagger</requirement> + <requirement type="package" version="0.3.4">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a |
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| diff -r d2009cdcdeba -r bf8ffb337cbe findcluster.xml --- a/findcluster.xml Fri Mar 03 10:30:14 2017 -0500 +++ b/findcluster.xml Sun Mar 05 13:29:42 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.3"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.4"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.3">readtagger</requirement> + <requirement type="package" version="0.3.4">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -10,6 +10,7 @@ --output_bam '$output_bam' --output_gff '$output_gff' --sample_name '$input.element_identifier' + --threads "\${GALAXY_SLOTS:-2}" ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> |
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| diff -r d2009cdcdeba -r bf8ffb337cbe test-data/three_cluster_out.bam |
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| Binary file test-data/three_cluster_out.bam has changed |
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| diff -r d2009cdcdeba -r bf8ffb337cbe test-data/three_cluster_out.gff --- a/test-data/three_cluster_out.gff Fri Mar 03 10:30:14 2017 -0500 +++ b/test-data/three_cluster_out.gff Sun Mar 05 13:29:42 2017 -0500 |
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| @@ -1,6 +1,4 @@ ##gff-version 3 -3R findcluster TE 13373515 13373524 39 + . ID=extended_and_annotated_roi.bam_0;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=26;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False -##gff-version 3 +3R findcluster TE 13373515 13373524 27 + . ID=extended_and_annotated_roi.bam_0;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False 3R findcluster TE 13374595 13374595 2 + . ID=extended_and_annotated_roi.bam_1;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;right_insert=;right_support=0;valid_TSD=False -##gff-version 3 3R findcluster TE 13374677 13374677 1 + . ID=extended_and_annotated_roi.bam_2;left_insert=;left_support=0;right_insert=;right_support=1;valid_TSD=False |