Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 34:5b08a7a4caa9 draft

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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 5dcad82862b4
children 5aa7745dd6e3
comparison
equal deleted inserted replaced
33:a01f2a172eeb 34:5b08a7a4caa9
1 <tool id="findcluster" name="Find clusters of reads" version="0.3.24"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.3.25">
2 <description>in bam files</description> 2 <description>in bam files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.3.24">readtagger</requirement> 7 <requirement type="package" version="0.3.25">readtagger</requirement>
5 </requirements> 8 </requirements>
6 <version_command>findcluster --version</version_command> 9 <version_command>findcluster --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
8 ln -f -s $input input.bam && 11 ln -f -s $input input.bam &&
9 ln -f -s $input.metadata.bam_index input.bam.bai && 12 ln -f -s $input.metadata.bam_index input.bam.bai &&
10 findcluster 13 findcluster
11 --input_path input.bam 14 --input_path input.bam
12 #if $transposon_reference_fasta: 15 #if $transposon_source.ref_file:
13 --transposon_reference_fasta '$transposon_reference_fasta' 16 #if str($transposon_source.reference_source_selector) == "history":
17 --transposon_reference_fasta '$transposon_source.ref_file'
18 #else :
19 --transposon_bwa_index '$reference_source.ref_file.fields.path'
20 #end if
14 #end if 21 #end if
15 #if $genome_reference_fasta: 22 #if $genome_source.ref_file:
16 --genome_reference_fasta '$genome_reference_fasta' 23 #if str($genome_source.reference_source_selector) == "history":
17 #end if 24 --genome_reference_fasta '$genome_source.ref_file'
18 #if $transposon_bwa_index: 25 #else :
19 --transposon_bwa_index '$transposon_bwa_index' 26 --genome_bwa_index '$reference_source.ref_file.fields.path'
20 #end if 27 #end if
21 #if $genome_bwa_index:
22 --genome_bwa_index '$genome_bwa_index'
23 #end if 28 #end if
24 --output_bam '$output_bam' 29 --output_bam '$output_bam'
25 --output_gff '$output_gff' 30 --output_gff '$output_gff'
26 --output_fasta '$output_fasta' 31 --output_fasta '$output_fasta'
27 --sample_name '$input.element_identifier' 32 --sample_name '$input.element_identifier'
28 --threads "\${GALAXY_SLOTS:-2}" 33 --threads "\${GALAXY_SLOTS:-2}"
29 ]]></command> 34 ]]></command>
30 <inputs> 35 <inputs>
31 <param name="input" argument="--input_path" type="data" format="bam"/> 36 <param name="input" argument="--input_path" type="data" format="bam"/>
32 <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"/> 37
33 <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"/> 38 <expand macro="reference_source_conditional" reference_type="transposon"/>
34 <param argument="--transposon_bwa_index" label="Transposon BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True"> 39 <expand macro="reference_source_conditional" reference_type="genome"/>
35 <options from_data_table="bwa_mem_indexes">
36 <filter type="sort_by" column="2" />
37 <validator type="no_options" message="No indexes are available" />
38 </options>
39 </param>
40 <param argument="--genome_bwa_index" label="Genome BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True">
41 <options from_data_table="bwa_mem_indexes">
42 <filter type="sort_by" column="2" />
43 <validator type="no_options" message="No indexes are available" />
44 </options>
45 </param>
46 </inputs> 40 </inputs>
47 <outputs> 41 <outputs>
48 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> 42 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
49 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/> 43 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
50 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> 44 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
55 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> 49 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
56 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> 50 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
57 </test> 51 </test>
58 <test> 52 <test>
59 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> 53 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
60 <param name="transposon_reference_fasta" value="reference.fasta" ftype="fasta"/> 54 <param name="transposon_source|reference_source_selector" value="history"/>
55 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
61 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> 56 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
62 <output name="output_gff"> 57 <output name="output_gff">
63 <assert_contents> 58 <assert_contents>
64 <has_text text="FBti0019066_rover_Gypsy" /> 59 <has_text text="FBti0019066_rover_Gypsy" />
65 </assert_contents> 60 </assert_contents>
71 66
72 Usage: findcluster [OPTIONS] 67 Usage: findcluster [OPTIONS]
73 68
74 Find clusters of reads that support a TE insertion. 69 Find clusters of reads that support a TE insertion.
75 70
76 Options: 71 Options:
77 --input_path PATH Find cluster in this BAM file. 72 --input_path PATH Find cluster in this BAM file.
73 --region TEXT Find clusters in this Region (Format is
74 chrX:2000-1000).
75 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
76 be inferred from the data.
78 --output_bam PATH Write out BAM file with cluster information 77 --output_bam PATH Write out BAM file with cluster information
79 to this path. Reads will have an additional 78 to this path. Reads will have an additional
80 "CD" tag to indicate the cluster number 79 "CD" tag to indicate the cluster number
81 --output_gff PATH Write out GFF file with cluster information 80 --output_gff PATH Write out GFF file with cluster information
81 to this path.
82 --output_fasta PATH Write out supporting evidence for clusters
82 to this path. 83 to this path.
83 --sample_name TEXT Sample name to use when writing out clusters 84 --sample_name TEXT Sample name to use when writing out clusters
84 in GFF file. Default is to infer the name 85 in GFF file. Default is to infer the name
85 from the input filename. 86 from the input filename.
86 --include_duplicates / --no-include_duplicates 87 --include_duplicates / --no-include_duplicates
87 Include reads marked as duplicates when 88 Include reads marked as duplicates when
88 finding clusters. 89 finding clusters.
89 --transposon_reference_fasta TEXT Blast cluster contigs against this fasta 90 --transposon_reference_fasta TEXT
90 file 91 Transposon fasta to align clipped reads to.
91 --blastdb TEXT Blast cluster contigs against this blast 92 Not necessary if BWA index is provided.
92 database 93 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
94 to
95 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
96 necessary if BWA index is provided.
97 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
93 --threads INTEGER RANGE Threads to use for cap3 assembly step 98 --threads INTEGER RANGE Threads to use for cap3 assembly step
99 --shm_dir PATH Path to shared memory folder
94 --version Show the version and exit. 100 --version Show the version and exit.
95 --help Show this message and exit. 101 --help Show this message and exit.
96 102
97 103
98 ]]></help> 104 ]]></help>