Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 32:5dcad82862b4 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 3cb122f0ab5dc2ad7bb61d1abdd13865142e25b8-dirty
author mvdbeek
date Wed, 21 Jun 2017 07:23:33 -0400
parents 5c32fb616d95
children 5b08a7a4caa9
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31
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parents: 30
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1 <tool id="findcluster" name="Find clusters of reads" version="0.3.24">
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2 <description>in bam files</description>
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3 <requirements>
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4 <requirement type="package" version="0.3.24">readtagger</requirement>
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5 </requirements>
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6 <version_command>findcluster --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 ln -f -s $input input.bam &&
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9 ln -f -s $input.metadata.bam_index input.bam.bai &&
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10 findcluster
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11 --input_path input.bam
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12 #if $transposon_reference_fasta:
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13 --transposon_reference_fasta '$transposon_reference_fasta'
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14 #end if
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15 #if $genome_reference_fasta:
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16 --genome_reference_fasta '$genome_reference_fasta'
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17 #end if
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18 #if $transposon_bwa_index:
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19 --transposon_bwa_index '$transposon_bwa_index'
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20 #end if
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21 #if $genome_bwa_index:
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parents: 31
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22 --genome_bwa_index '$genome_bwa_index'
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23 #end if
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24 --output_bam '$output_bam'
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25 --output_gff '$output_gff'
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26 --output_fasta '$output_fasta'
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27 --sample_name '$input.element_identifier'
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28 --threads "\${GALAXY_SLOTS:-2}"
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29 ]]></command>
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30 <inputs>
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31 <param name="input" argument="--input_path" type="data" format="bam"/>
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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"/>
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parents: 31
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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"/>
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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">
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35 <options from_data_table="bwa_mem_indexes">
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mvdbeek
parents: 31
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36 <filter type="sort_by" column="2" />
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mvdbeek
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37 <validator type="no_options" message="No indexes are available" />
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parents: 31
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38 </options>
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39 </param>
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parents: 31
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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">
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parents: 31
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41 <options from_data_table="bwa_mem_indexes">
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42 <filter type="sort_by" column="2" />
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43 <validator type="no_options" message="No indexes are available" />
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44 </options>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
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49 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
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50 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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55 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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56 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
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57 </test>
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58 <test>
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59 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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60 <param name="transposon_reference_fasta" value="reference.fasta" ftype="fasta"/>
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61 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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62 <output name="output_gff">
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63 <assert_contents>
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64 <has_text text="FBti0019066_rover_Gypsy" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 .. code-block::
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71
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72 Usage: findcluster [OPTIONS]
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73
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74 Find clusters of reads that support a TE insertion.
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75
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76 Options:
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77 --input_path PATH Find cluster in this BAM file.
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78 --output_bam PATH Write out BAM file with cluster information
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79 to this path. Reads will have an additional
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
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80 "CD" tag to indicate the cluster number
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81 --output_gff PATH Write out GFF file with cluster information
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parents: 11
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82 to this path.
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83 --sample_name TEXT Sample name to use when writing out clusters
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parents: 11
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84 in GFF file. Default is to infer the name
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85 from the input filename.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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86 --include_duplicates / --no-include_duplicates
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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87 Include reads marked as duplicates when
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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88 finding clusters.
32
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89 --transposon_reference_fasta TEXT Blast cluster contigs against this fasta
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
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90 file
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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91 --blastdb TEXT Blast cluster contigs against this blast
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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92 database
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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93 --threads INTEGER RANGE Threads to use for cap3 assembly step
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
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94 --version Show the version and exit.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
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95 --help Show this message and exit.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
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96
5
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97
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98 ]]></help>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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99 </tool>