Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 39:432bb619c079 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
author mvdbeek
date Thu, 15 Mar 2018 07:20:58 -0400
parents f6311a04a6c9
children 4b1ebfcd0f46
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1 <tool id="findcluster" name="Find clusters of reads" version="0.4.9">
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2 <description>in bam files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.4.9">readtagger</requirement>
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8 </requirements>
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9 <version_command>findcluster --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #import re
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12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
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13 ln -f -s $input input.bam &&
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14 ln -f -s $input.metadata.bam_index input.bam.bai &&
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15 findcluster
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16 --input_path input.bam
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17 #if $transposon_source.ref_file:
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18 #if str($transposon_source.reference_source_selector) == "history":
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19 --transposon_reference_fasta '$transposon_source.ref_file'
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20 #else :
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21 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
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22 #end if
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23 #end if
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24 #if $genome_source.ref_file:
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25 #if str($genome_source.reference_source_selector) == "history":
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26 --genome_reference_fasta '$genome_source.ref_file'
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27 #else :
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28 --genome_bwa_index '$genome_source.ref_file.fields.path'
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29 #end if
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30 #end if
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31 --output_bam '$output_bam'
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32 --output_gff '$output_gff'
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33 --output_fasta '$output_fasta'
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34 --sample_name '$sample_name'
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35 --threads "\${GALAXY_SLOTS:-2}"
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36 ]]></command>
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37 <inputs>
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38 <param name="input" argument="--input_path" type="data" format="bam"/>
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40 <expand macro="reference_source_conditional" reference_type="transposon"/>
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41 <expand macro="reference_source_conditional" reference_type="genome"/>
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42 </inputs>
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43 <outputs>
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44 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
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45 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
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46 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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51 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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52 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0" sort="True"/>
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53 </test>
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54 <test>
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55 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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56 <param name="transposon_source|reference_source_selector" value="history"/>
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57 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
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58 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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59 <output name="output_gff">
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60 <assert_contents>
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61 <has_text text="FBti0019066_rover_Gypsy" />
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 .. code-block::
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68
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69 Usage: findcluster [OPTIONS]
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70
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71 Find clusters of reads that support a TE insertion.
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72
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73 Options:
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74 --input_path PATH Find cluster in this BAM file.
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75 --region TEXT Find clusters in this Region (Format is
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76 chrX:2000-1000).
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77 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
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78 be inferred from the data.
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79 --output_bam PATH Write out BAM file with cluster information
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80 to this path. Reads will have an additional
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81 "CD" tag to indicate the cluster number
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82 --output_gff PATH Write out GFF file with cluster information
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83 to this path.
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84 --output_fasta PATH Write out supporting evidence for clusters
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85 to this path.
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parents: 10
diff changeset
86 --sample_name TEXT Sample name to use when writing out clusters
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
87 in GFF file. Default is to infer the name
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
88 from the input filename.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
89 --include_duplicates / --no-include_duplicates
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
90 Include reads marked as duplicates when
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
91 finding clusters.
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
92 --transposon_reference_fasta TEXT
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
93 Transposon fasta to align clipped reads to.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
94 Not necessary if BWA index is provided.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
95 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
96 to
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
97 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
98 necessary if BWA index is provided.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
99 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
100 --threads INTEGER RANGE Threads to use for cap3 assembly step
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
101 --shm_dir PATH Path to shared memory folder
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
102 --version Show the version and exit.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
103 --help Show this message and exit.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
104
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
105
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
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106 ]]></help>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
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107 </tool>