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annotate manta_macros.xml @ 0:42ba283a0fe2 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
author artbio
date Wed, 13 May 2020 15:15:07 -0400
parents
children c35d9902100e
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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1 <macros>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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3 <token name="@VERSION@">1.6</token>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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5 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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7 <token name="@set_reference_fasta_filename@"><![CDATA[
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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8 #set $reference_fasta_filename = "localref.fa"
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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9
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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10 #if str( $reference_source.reference_source_selector ) == "history":
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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11 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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12 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 &&
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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13 #else:
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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14 #set $reference_fasta_filename = str( $reference_source.index.fields.path )
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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15 #end if
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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16 ]]></token>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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18 <token name="@set_configuration_file@"><![CDATA[
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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19 #if str( $configuration.configuration_switch ) == "Custom_config_file":
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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20 #set $config_file = '$configuration.CustomConfigFile'
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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21 #else if str( $configuration.configuration_switch )== "Customized":
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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22 #set $config_file = '$configuration.Customized'
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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23 #else:
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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24 #set $config_file = $__tool_directory__ + '/configManta.py.ini'
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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25 #end if
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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26 ]]></token>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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29 <xml name="requirements">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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30 <requirements>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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31 <requirement type="package" version="1.7">samtools</requirement>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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32 <requirement type="package" version="@VERSION@">manta</requirement>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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33 </requirements>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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34 </xml>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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36 <xml name="stdio">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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37 <stdio>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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38 <exit_code range="1:" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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39 <exit_code range=":-1" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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40 <regex match="Error:" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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41 <regex match="Exception:" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42 <regex match="\[bns_restore_core\] Parse error reading" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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43 </stdio>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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44 </xml>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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45
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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46 <macro name="reference_source_conditional">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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47 <conditional name="reference_source">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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48 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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49 <option value="cached">Use a built-in genome index</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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50 <option value="history">Use a genome from history and build index</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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51 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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52 <when value="cached">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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53 <param name="index" type="select" label="Using reference genome" help="Select genome from the list">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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54 <options from_data_table="all_fasta">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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55 <filter type="sort_by" column="2" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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56 <validator type="no_options" message="No indexes are available" />
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57 </options>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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58 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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59 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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60 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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61 <when value="history">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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62 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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63 help="You can upload a FASTA sequence to the history and use it as reference" />
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64 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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65 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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66 </macro>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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67
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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68 <macro name="manta_configuration">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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69 <conditional name="configuration">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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70 <param name="configuration_switch" type="select" label="How do you want to configure manta?">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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71 <option value="Custom_config_file">Upload a different config file</option>
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72 <option value="Customized">Customize the options</option>
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73 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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74 <when value="Custom_config_file">
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75 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
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76 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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77 <when value="Customized">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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78 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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79 <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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80 <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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81 <param name="graphNodeMaxEdgeCount" type="integer" value="10" label="graphNodeMaxEdgeCount" help="If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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82 <param name="minCandidateSpanningCount" type="integer" value="3" label="minCandidateSpanningCount" help="Run discovery and candidate reporting for all SVs/indels with at least this many spanning support observations."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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83 <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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84 <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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85 <param name="minPassDiploidVariantScore" type="integer" value="20" label="minPassDiploidVariantScore" help="VCF 'QUAL' score below which a variant is marked as filtered in the diploid vcf."/>
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86 <param name="minPassDiploidGTScore" type="integer" value="15" label="minPassDiploidGTScore" help="Minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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87 <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/>
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88 <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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89 <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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90 <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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91 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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92 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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93 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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94 </macro>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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95
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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96 </macros>