Mercurial > repos > mvdbeek > bam_readtagger
changeset 34:5b08a7a4caa9 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
| author | mvdbeek |
|---|---|
| date | Wed, 21 Jun 2017 09:38:09 -0400 |
| parents | a01f2a172eeb |
| children | 5aa7745dd6e3 |
| files | add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml deploy.sh findcluster.xml macros.xml update_mapq.xml write_supplementary_fastq.xml |
| diffstat | 7 files changed, 68 insertions(+), 42 deletions(-) [+] |
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--- a/add_matesequence.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/add_matesequence.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="add_matesequence" name="Add matesequence" version="0.3.24"> +<tool id="add_matesequence" name="Add matesequence" version="0.3.25"> <description>into tag field</description> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/allow_dovetailing.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.24"> +<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.25"> <description>modifies proper_pair flag in bam files</description> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/bam_readtagger.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,10 +1,10 @@ -<tool id="bam_readtagger" name="Tag alignment files" version="0.3.24"> +<tool id="bam_readtagger" name="Tag alignment files" version="0.3.25"> <description>from multiple bam files</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ readtagger -t '$tag_file' -s
--- a/findcluster.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/findcluster.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,7 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.24"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.25"> <description>in bam files</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -9,17 +12,19 @@ ln -f -s $input.metadata.bam_index input.bam.bai && findcluster --input_path input.bam - #if $transposon_reference_fasta: - --transposon_reference_fasta '$transposon_reference_fasta' - #end if - #if $genome_reference_fasta: - --genome_reference_fasta '$genome_reference_fasta' + #if $transposon_source.ref_file: + #if str($transposon_source.reference_source_selector) == "history": + --transposon_reference_fasta '$transposon_source.ref_file' + #else : + --transposon_bwa_index '$reference_source.ref_file.fields.path' + #end if #end if - #if $transposon_bwa_index: - --transposon_bwa_index '$transposon_bwa_index' - #end if - #if $genome_bwa_index: - --genome_bwa_index '$genome_bwa_index' + #if $genome_source.ref_file: + #if str($genome_source.reference_source_selector) == "history": + --genome_reference_fasta '$genome_source.ref_file' + #else : + --genome_bwa_index '$reference_source.ref_file.fields.path' + #end if #end if --output_bam '$output_bam' --output_gff '$output_gff' @@ -29,20 +34,9 @@ ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> - <param argument="--transposon_reference_fasta" label="Transposon Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/> - <param argument="--genome_reference_fasta" label="Genome Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/> - <param argument="--transposon_bwa_index" label="Transposon BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True"> - <options from_data_table="bwa_mem_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - <param argument="--genome_bwa_index" label="Genome BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True"> - <options from_data_table="bwa_mem_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> + + <expand macro="reference_source_conditional" reference_type="transposon"/> + <expand macro="reference_source_conditional" reference_type="genome"/> </inputs> <outputs> <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> @@ -57,7 +51,8 @@ </test> <test> <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> - <param name="transposon_reference_fasta" value="reference.fasta" ftype="fasta"/> + <param name="transposon_source|reference_source_selector" value="history"/> + <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/> <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> <output name="output_gff"> <assert_contents> @@ -73,24 +68,35 @@ Find clusters of reads that support a TE insertion. - Options: + Options: --input_path PATH Find cluster in this BAM file. + --region TEXT Find clusters in this Region (Format is + chrX:2000-1000). + --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will + be inferred from the data. --output_bam PATH Write out BAM file with cluster information to this path. Reads will have an additional "CD" tag to indicate the cluster number --output_gff PATH Write out GFF file with cluster information to this path. + --output_fasta PATH Write out supporting evidence for clusters + to this path. --sample_name TEXT Sample name to use when writing out clusters in GFF file. Default is to infer the name from the input filename. --include_duplicates / --no-include_duplicates Include reads marked as duplicates when finding clusters. - --transposon_reference_fasta TEXT Blast cluster contigs against this fasta - file - --blastdb TEXT Blast cluster contigs against this blast - database + --transposon_reference_fasta TEXT + Transposon fasta to align clipped reads to. + Not necessary if BWA index is provided. + --transposon_bwa_index TEXT Transposon BWA index to align clipped reads + to + --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not + necessary if BWA index is provided. + --genome_bwa_index TEXT Genome BWA index to align clipped reads to --threads INTEGER RANGE Threads to use for cap3 assembly step + --shm_dir PATH Path to shared memory folder --version Show the version and exit. --help Show this message and exit.
--- a/macros.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/macros.xml Wed Jun 21 09:38:09 2017 -0400 @@ -26,4 +26,24 @@ <option value="X">X</option> <option value="Y">Y</option> </xml> + <xml name="reference_source_conditional" token_reference_type="reference_type"> + <conditional name="@REFERENCE_TYPE@_source"> + <param name="reference_source_selector" type="select" label="Will you select a @REFERENCE_TYPE@ reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <option value="cached">Use a built-in @REFERENCE_TYPE@ genome index</option> + <option value="history">Use a genome from history and build index</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using @REFERENCE_TYPE@ reference genome" help="Select @REFERENCE_TYPE@ genome from the list" optional="True"> + <options from_data_table="bwa_mem_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" optional="True"/> + </when> + </conditional> + </xml> </macros>
--- a/update_mapq.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/update_mapq.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="update_mapq" name="Update MAPQ score" version="0.3.24"> +<tool id="update_mapq" name="Update MAPQ score" version="0.3.25"> <description>of supplementary alignments</description> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <version_command>update_mapq --version</version_command> <command detect_errors="aggressive"><![CDATA[
--- a/write_supplementary_fastq.xml Wed Jun 21 07:24:36 2017 -0400 +++ b/write_supplementary_fastq.xml Wed Jun 21 09:38:09 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.24"> +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.25"> <description>from SAM/BAM alignment files as FASTQ</description> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <version_command>write_supplementary_fastq --version</version_command> <command detect_errors="aggressive"><![CDATA[