Mercurial > repos > mvdbeek > bam_readtagger
comparison findcluster.xml @ 31:301316cb596a draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
author | mvdbeek |
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date | Wed, 21 Jun 2017 09:38:25 -0400 |
parents | db5c766503dd |
children | bf3d04937095 |
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30:db5c766503dd | 31:301316cb596a |
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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 $reference_fasta: | 15 #if $transposon_source.ref_file: |
13 --reference_fasta '$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 | |
21 #end if | |
22 #if $genome_source.ref_file: | |
23 #if str($genome_source.reference_source_selector) == "history": | |
24 --genome_reference_fasta '$genome_source.ref_file' | |
25 #else : | |
26 --genome_bwa_index '$reference_source.ref_file.fields.path' | |
27 #end if | |
14 #end if | 28 #end if |
15 --output_bam '$output_bam' | 29 --output_bam '$output_bam' |
16 --output_gff '$output_gff' | 30 --output_gff '$output_gff' |
17 --output_fasta '$output_fasta' | 31 --output_fasta '$output_fasta' |
18 --sample_name '$input.element_identifier' | 32 --sample_name '$input.element_identifier' |
19 --threads "\${GALAXY_SLOTS:-2}" | 33 --threads "\${GALAXY_SLOTS:-2}" |
20 ]]></command> | 34 ]]></command> |
21 <inputs> | 35 <inputs> |
22 <param name="input" argument="--input_path" type="data" format="bam"/> | 36 <param name="input" argument="--input_path" type="data" format="bam"/> |
23 <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/> | 37 |
38 <expand macro="reference_source_conditional" reference_type="transposon"/> | |
39 <expand macro="reference_source_conditional" reference_type="genome"/> | |
24 </inputs> | 40 </inputs> |
25 <outputs> | 41 <outputs> |
26 <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"/> |
27 <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"/> |
28 <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"/> |
33 <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"/> |
34 <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"/> |
35 </test> | 51 </test> |
36 <test> | 52 <test> |
37 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> | 53 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> |
38 <param name="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"/> | |
39 <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"/> |
40 <output name="output_gff"> | 57 <output name="output_gff"> |
41 <assert_contents> | 58 <assert_contents> |
42 <has_text text="FBti0019066_rover_Gypsy" /> | 59 <has_text text="FBti0019066_rover_Gypsy" /> |
43 </assert_contents> | 60 </assert_contents> |
49 | 66 |
50 Usage: findcluster [OPTIONS] | 67 Usage: findcluster [OPTIONS] |
51 | 68 |
52 Find clusters of reads that support a TE insertion. | 69 Find clusters of reads that support a TE insertion. |
53 | 70 |
54 Options: | 71 Options: |
55 --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. | |
56 --output_bam PATH Write out BAM file with cluster information | 77 --output_bam PATH Write out BAM file with cluster information |
57 to this path. Reads will have an additional | 78 to this path. Reads will have an additional |
58 "CD" tag to indicate the cluster number | 79 "CD" tag to indicate the cluster number |
59 --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 | |
60 to this path. | 83 to this path. |
61 --sample_name TEXT Sample name to use when writing out clusters | 84 --sample_name TEXT Sample name to use when writing out clusters |
62 in GFF file. Default is to infer the name | 85 in GFF file. Default is to infer the name |
63 from the input filename. | 86 from the input filename. |
64 --include_duplicates / --no-include_duplicates | 87 --include_duplicates / --no-include_duplicates |
65 Include reads marked as duplicates when | 88 Include reads marked as duplicates when |
66 finding clusters. | 89 finding clusters. |
67 --reference_fasta TEXT Blast cluster contigs against this fasta | 90 --transposon_reference_fasta TEXT |
68 file | 91 Transposon fasta to align clipped reads to. |
69 --blastdb TEXT Blast cluster contigs against this blast | 92 Not necessary if BWA index is provided. |
70 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 | |
71 --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 | |
72 --version Show the version and exit. | 100 --version Show the version and exit. |
73 --help Show this message and exit. | 101 --help Show this message and exit. |
74 | 102 |
75 | 103 |
76 ]]></help> | 104 ]]></help> |