| Previous changeset 33:c7f140920cc1 (2017-11-09) Next changeset 35:02afdbc69591 (2017-12-14) |
|
Commit message:
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty |
|
modified:
add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml update_mapq.xml write_supplementary_fastq.xml |
|
added:
plot_coverage.xml test-data/three_cluster_plot.pdf |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 add_matesequence.xml --- a/add_matesequence.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/add_matesequence.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.4.0"> +<tool id="add_matesequence" name="Add matesequence" version="0.4.1"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 allow_dovetailing.xml --- a/allow_dovetailing.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/allow_dovetailing.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.0"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.1"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output' |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 bam_readtagger.xml --- a/bam_readtagger.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/bam_readtagger.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.4.0"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.4.1"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 findcluster.xml --- a/findcluster.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/findcluster.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,13 +1,15 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.4.0"> +<tool id="findcluster" name="Find clusters of reads" version="0.4.1"> <description>in bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ + #import re + #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) ln -f -s $input input.bam && ln -f -s $input.metadata.bam_index input.bam.bai && findcluster @@ -29,7 +31,7 @@ --output_bam '$output_bam' --output_gff '$output_gff' --output_fasta '$output_fasta' - --sample_name '$input.element_identifier' + --sample_name '$sample_name' --threads "\${GALAXY_SLOTS:-2}" ]]></command> <inputs> |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 plot_coverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_coverage.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +<tool id="plot_coverage" name="Plot coverage" version="0.4.1"> + <description>as area plot between BAM files</description> + <requirements> + <requirement type="package" version="0.4.1">readtagger</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + #import re + #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier)) + #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier)) + plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' + ]]></command> + <inputs> + <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/> + <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/> + <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="-" /> + <add value="," /> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> + </outputs> + <tests> + <test> + <param name="input1" value="three_cluster_out.bam" ftype="bam"/> + <param name="input2" value="three_cluster_out.bam" ftype="bam"/> + <param name="regions" value="3R:13373525-13373615"/> + <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +This tool plots the coverage over a specified region (by default all chromosomes/contigs). + + ]]></help> +</tool> |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 test-data/three_cluster_plot.pdf |
| b |
| Binary file test-data/three_cluster_plot.pdf has changed |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 update_mapq.xml --- a/update_mapq.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/update_mapq.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.4.0"> +<tool id="update_mapq" name="Update MAPQ score" version="0.4.1"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |
| b |
| diff -r c7f140920cc1 -r 240c901dedc0 write_supplementary_fastq.xml --- a/write_supplementary_fastq.xml Thu Nov 09 06:49:15 2017 -0500 +++ b/write_supplementary_fastq.xml Mon Nov 20 10:50:42 2017 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.0"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.1"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.4.0">readtagger</requirement> + <requirement type="package" version="0.4.1">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[ |