| Previous changeset 3:cb9036583afe (2017-02-21) Next changeset 5:a3c2c0f6abc9 (2017-03-02) |
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Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml |
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added:
findcluster.xml test-data/extended_and_annotated_roi.bam test-data/tagged_dm6.bam test-data/three_cluster_out.bam test-data/three_cluster_out.gff |
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removed:
test.sh |
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| diff -r cb9036583afe -r 7625c594bc37 add_matesequence.xml --- a/add_matesequence.xml Tue Feb 21 04:39:31 2017 -0500 +++ b/add_matesequence.xml Thu Mar 02 09:02:27 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.2.0"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.0"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.2.0">readtagger</requirement> + <requirement type="package" version="0.3.0">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r cb9036583afe -r 7625c594bc37 allow_dovetailing.xml --- a/allow_dovetailing.xml Tue Feb 21 04:39:31 2017 -0500 +++ b/allow_dovetailing.xml Thu Mar 02 09:02:27 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.2.0"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.0"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.2.0">readtagger</requirement> + <requirement type="package" version="0.3.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r cb9036583afe -r 7625c594bc37 bam_readtagger.xml --- a/bam_readtagger.xml Tue Feb 21 04:39:31 2017 -0500 +++ b/bam_readtagger.xml Thu Mar 02 09:02:27 2017 -0500 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.2.0"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.0"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.2.0">readtagger</requirement> + <requirement type="package" version="0.3.0">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -a |
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| diff -r cb9036583afe -r 7625c594bc37 findcluster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findcluster.xml Thu Mar 02 09:02:27 2017 -0500 |
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| @@ -0,0 +1,47 @@ +<tool id="findcluster" name="Find clusters of reads" version="0.3.0"> + <description>in bam files</description> + <requirements> + <requirement type="package" version="0.3.0">readtagger</requirement> + </requirements> + <version_command>findcluster --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + findcluster + --input_path '$input' + --output_bam '$output_bam' + --output_gff '$output_gff' + --sample_name '$input.element_identifier' + ]]></command> + <inputs> + <param name="input" argument="--input_path" type="data" format="bam"/> + </inputs> + <outputs> + <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> + <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> + </outputs> + <tests> + <test> + <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> + <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> + <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> + </test> + </tests> + <help><![CDATA[ +.. code-block:: + + Find clusters of reads that support a TE insertion. + + optional arguments: + -h, --help show this help message and exit + --input_path INPUT_PATH + Find cluster in this BAM file. (default: None) + --output_bam OUTPUT_BAM + Write out BAM file with cluster information to this + path. Reads will have an additional "CD" tag to + indicate the cluster number (default: None) + --output_gff OUTPUT_GFF + Write out GFF file with cluster information to this + path. (default: None) + --version show program's version number and exit + +]]></help> +</tool> |
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| diff -r cb9036583afe -r 7625c594bc37 test-data/extended_and_annotated_roi.bam |
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| Binary file test-data/extended_and_annotated_roi.bam has changed |
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| diff -r cb9036583afe -r 7625c594bc37 test-data/tagged_dm6.bam |
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| Binary file test-data/tagged_dm6.bam has changed |
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| diff -r cb9036583afe -r 7625c594bc37 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 cb9036583afe -r 7625c594bc37 test-data/three_cluster_out.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_cluster_out.gff Thu Mar 02 09:02:27 2017 -0500 |
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| @@ -0,0 +1,6 @@ +##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 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 |
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| diff -r cb9036583afe -r 7625c594bc37 test.sh --- a/test.sh Tue Feb 21 04:39:31 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -#!/usr/bin/env bash - -set -e - -if grep -v 'python tag_reads.py' bam_tag_reads.xml -then - sed -i.bak 's/tag_reads -t/python \$__tool_directory__\/tag_reads.py -t/g' bam_tag_reads.xml -fi -cp ../tag_reads/tag_reads.py . -planemo test --conda_prefix ~/miniconda3 |