Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 24:9c7b5c905920 draft

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author mvdbeek
date Tue, 25 Apr 2017 14:54:13 -0400
parents 1323ffbc8785
children 6492af8015a6
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1 <tool id="findcluster" name="Find clusters of reads" version="0.3.18">
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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="0.3.18">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 $reference_fasta:
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13 --reference_fasta '$reference_fasta'
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14 #end if
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15 --output_bam '$output_bam'
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16 --output_gff '$output_gff'
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17 --output_fasta '$output_fasta'
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18 --sample_name '$input.element_identifier'
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19 --threads "\${GALAXY_SLOTS:-2}"
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20 ]]></command>
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21 <inputs>
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22 <param name="input" argument="--input_path" type="data" format="bam"/>
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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"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
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27 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
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28 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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33 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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34 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
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35 </test>
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36 <test>
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37 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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38 <param name="reference_fasta" value="reference.fasta" ftype="fasta"/>
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39 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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40 <output name="output_gff">
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41 <assert_contents>
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42 <has_text text="FBti0019066_rover_Gypsy" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 .. code-block::
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49
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50 Usage: findcluster [OPTIONS]
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51
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52 Find clusters of reads that support a TE insertion.
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53
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54 Options:
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55 --input_path PATH Find cluster in this BAM file.
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56 --output_bam PATH Write out BAM file with cluster information
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57 to this path. Reads will have an additional
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58 "CD" tag to indicate the cluster number
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59 --output_gff PATH Write out GFF file with cluster information
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60 to this path.
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61 --sample_name TEXT Sample name to use when writing out clusters
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62 in GFF file. Default is to infer the name
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63 from the input filename.
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64 --include_duplicates / --no-include_duplicates
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65 Include reads marked as duplicates when
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66 finding clusters.
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67 --reference_fasta TEXT Blast cluster contigs against this fasta
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68 file
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69 --blastdb TEXT Blast cluster contigs against this blast
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70 database
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71 --threads INTEGER RANGE Threads to use for cap3 assembly step
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72 --version Show the version and exit.
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73 --help Show this message and exit.
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74
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75
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76 ]]></help>
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77 </tool>