Mercurial > repos > mvdbeek > bam_readtagger

changeset 64:190d64e5e32b draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be63fdf98ea1aaa5009136c6b0f8c1311e53bb8e"
author mvdbeek
date Sun, 01 Sep 2019 16:30:54 -0400
parents e675e6d349bd
children da97e0316abc
files 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
diffstat 10 files changed, 24 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/add_matesequence.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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[
--- a/allow_dovetailing.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/allow_dovetailing.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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'
--- a/bam_readtagger.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/bam_readtagger.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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 '$tag_file' -s
--- a/extract_variants.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/extract_variants.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.10">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.11">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.10">readtagger</requirement>
+        <requirement type="package" version="0.5.11">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/filter_insertions.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/filter_insertions.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.10">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.11">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.10">readtagger</requirement>
+        <requirement type="package" version="0.5.11">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -18,12 +18,14 @@
         #end for
         --output_path '$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"/>
--- a/findcluster.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/findcluster.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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[
--- a/plot_coverage.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/plot_coverage.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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
--- 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
@@ -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
--- a/update_mapq.xml	Sun Sep 01 12:03:42 2019 -0400
+++ b/update_mapq.xml	Sun Sep 01 16:30:54 2019 -0400
@@ -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[
--- 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
@@ -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[