| Previous changeset 63:e675e6d349bd (2019-09-01) Next changeset 65:da97e0316abc (2019-09-02) |
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Commit message:
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be63fdf98ea1aaa5009136c6b0f8c1311e53bb8e" |
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modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml extract_variants.xml filter_insertions.xml findcluster.xml plot_coverage.xml test-data/confirmed_insertions.gff update_mapq.xml write_supplementary_fastq.xml |
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| diff -r e675e6d349bd -r 190d64e5e32b add_matesequence.xml --- a/add_matesequence.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/add_matesequence.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.5.10"> +<tool id="add_matesequence" name="Add matesequence" version="0.5.11"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r e675e6d349bd -r 190d64e5e32b allow_dovetailing.xml --- a/allow_dovetailing.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/allow_dovetailing.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.10"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.11"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
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| diff -r e675e6d349bd -r 190d64e5e32b bam_readtagger.xml --- a/bam_readtagger.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/bam_readtagger.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.5.10"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.5.11"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
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| diff -r e675e6d349bd -r 190d64e5e32b extract_variants.xml --- a/extract_variants.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/extract_variants.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="extract_variants" name="Extract variant fragments" version="0.5.10"> +<tool id="extract_variants" name="Extract variant fragments" version="0.5.11"> <description>from long reads</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r e675e6d349bd -r 190d64e5e32b filter_insertions.xml --- a/filter_insertions.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/filter_insertions.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.10"> +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.11"> <description>based on softclips in control files</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -18,12 +18,14 @@ #end for --output_path '$output' $output_discard + --min_length $min_length ]]></command> <inputs> <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/> <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> + <param argument="--min_length" label="Minimum length necessary to match clip patterns" help="If too low will create false matches, if too high will not find legitimate matches." value="4" min="1" type="integer"/> </inputs> <outputs> <data name="output" format="gff3"/> |
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| diff -r e675e6d349bd -r 190d64e5e32b findcluster.xml --- a/findcluster.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/findcluster.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,10 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.5.10"> +<tool id="findcluster" name="Find clusters of reads" version="0.5.11"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r e675e6d349bd -r 190d64e5e32b plot_coverage.xml --- a/plot_coverage.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/plot_coverage.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.10"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.11"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #import re |
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| diff -r e675e6d349bd -r 190d64e5e32b test-data/confirmed_insertions.gff --- a/test-data/confirmed_insertions.gff Sun Sep 01 12:03:42 2019 -0400 +++ b/test-data/confirmed_insertions.gff Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,4 +1,4 @@ -2R findcluster jockey2 16727068 16727111 6 + . ID=R37_27;softclip_clusters=softclip_test1 -TEST findcluster jockey2 16727068 16727111 6 + . ID=R37_27;softclip_clusters=softclip_test1 -X findcluster transposable_element_rover 10766937 10766942 24 + . ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True -X findcluster jockey2 16727068 16727111 6 + . ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_matches_softclip_0 +2R findcluster jockey2 16727068 16727111 6 + . ID=R37_27;softclip_clusters=softclip_test1;overlaps= +TEST findcluster jockey2 16727068 16727111 6 + . ID=R37_27;softclip_clusters=softclip_test1;overlaps= +X findcluster transposable_element_rover 10766937 10766942 24 + . ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True;overlaps= +X findcluster jockey2 16727068 16727111 6 + . ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;softclip_clusters=softclip_2,softclip_3;total_left_count=3;total_right_count=4;valid_TSD=True;overlaps=;FAIL=clip_seq_matches_softclip_0 |
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| diff -r e675e6d349bd -r 190d64e5e32b update_mapq.xml --- a/update_mapq.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/update_mapq.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.5.10"> +<tool id="update_mapq" name="Update MAPQ score" version="0.5.11"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
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| diff -r e675e6d349bd -r 190d64e5e32b write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Sun Sep 01 12:03:42 2019 -0400 +++ b/write_supplementary_fastq.xml Sun Sep 01 16:30:54 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.10"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.11"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.5.10">readtagger</requirement> + <requirement type="package" version="0.5.11">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |