Mercurial > repos > mvdbeek > tepid_discover

annotate tepid-discover.xml @ 0:a5ef6470e54d draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
author mvdbeek
date Thu, 15 Dec 2016 08:33:53 -0500
parents
children cea423bd0cd2
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0
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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1 <tool id="tepid_discover" name="tepid-discover" version="@WRAPPER_VERSION@">
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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2 <description>discover TE variants</description>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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3 <macros>
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mvdbeek
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4 <import>macros.xml</import>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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5 </macros>
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mvdbeek
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6 <expand macro="requirements"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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7 <version_command>tepid-discover --version</version_command>
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mvdbeek
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8 <command detect_errors="exit_code"><![CDATA[
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mvdbeek
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9 @LINK_CONC@
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mvdbeek
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10 tepid-discover
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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11 $deletions
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12 $insertions
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13 $strict
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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14 #if $mask:
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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15 --mask '$mask'
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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16 #end if
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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17 #if $discordant_bam:
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18 --discordant '$discordant_bam'
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mvdbeek
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19 #end if
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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20 @PROC@
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21 @NAME@
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22 -c conc.bam
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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23 -s '$split_bam'
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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24 -t '$te_annotation_bed'
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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25 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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26 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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27 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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28 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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29 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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30 cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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31 ]]></command>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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32 <inputs>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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33 <param name="bowtie2_bam" label="Alignment file (Bowtie2)" argument="--conc" type="data" format="bam"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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34 <param name="discordant_bam" label="Alignment file with discordant pairs" argument="--discordant" optional="true" type="data" format="bam"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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35 <param name="split_bam" label="Alignment file with split reads" argument="--split" type="data" format="bam"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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36 <param name="mask" type="select" optional="True" label="Select chromosomes that you would like to exclude" multiple="True">
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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37 <options>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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38 <filter type="data_meta" ref="bowtie2_bam" key="reference_names" />
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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39 </options>
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mvdbeek
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40 </param>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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41 <param name="te_annotation_bed" label="BED file with TE locations" argument="--te" type="data" format="bed"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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42 <param name="se_mode" argument="--se" type="boolean" truevalue="--se" falsevalue="" label="Run in single-end mode?"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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43 <param name="deletions" argument="--deletions" type="boolean" truevalue="--deletions" falsevalue="" label="Find deletions only?"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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44 <param name="insertions" argument="--insertions" type="boolean" truevalue="--insertions" falsevalue="" label="Find insertions only?"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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45 <param name="strict" argument="--strict" type="boolean" truevalue="--strict" falsevalue="" label="Report high-confidence variants only?"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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46 </inputs>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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47 <outputs>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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48 <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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49 <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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50 <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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51 <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="bowtie2_bam" value="conc.bam"/>
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56 <param name="split_bam" value="split.bam"/>
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mvdbeek
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57 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
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mvdbeek
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58 <output name="insertions_out" file="insertions_test.bed"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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59 <output name="deletions_out" file="deletions_test.bed"/>
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mvdbeek
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60 <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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61 <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
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62 </test>
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63 </tests>
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mvdbeek
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64 <help><![CDATA[
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65 TEPID -- transposable element polymorphism identification
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66
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67 optional arguments:
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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68 -h, --help show this help message and exit
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69 --version show program's version number and exit
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70 -k, --keep keep all intermediate files
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71 -d, --deletions find deletions only
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
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72 -i, --insertions find insertions only
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73 --strict Report high-confidence variants only
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74 --mask MASK Mask chromosomes in comma separated list or file
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75 -D DISCORDANT, --discordant DISCORDANT
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76 Supply discordant reads bam file
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77 -p PROC, --proc PROC number of processors
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78 -n NAME, --name NAME sample name
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79 -c CONC, --conc CONC bam file from bowtie2
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80 -s SPLIT, --split SPLIT
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81 split reads bam file from yaha
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82 -t TE, --te TE TE annotation bedfile
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mvdbeek
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83 --se Run in single-end mode
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84 ]]></help>
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85 <expand macro="citations"/>
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86 </tool>