Mercurial > repos > matthias > stacks2_cstacks

annotate macros_process.xml @ 2:8427e904f352 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:52:48 -0500
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children 924e7889aa05
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2
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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1 <?xml version="1.0"?>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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2
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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3 <!-- macros and tokens for process_radtags and process_short_reads -->
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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4
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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5 <macros>
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6 <!-- fastq input for process_radtags/shortreads-->
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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7 <xml name="process_inputs">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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8 <conditional name="input_type">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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9 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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10 <option value="single" selected="True">Single-end files</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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11 <option value="paired">Paired-end files</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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12 </param>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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13 <when value="single">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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14 <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz" multiple="true" type="data" label="singles-end reads infile(s)" help="input files" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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15 <param name="barcode_encoding" type="select" label="Barcode location">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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16 <expand macro="barcode_encoding_single" type="Barcode" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
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17 </param>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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18 </when>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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19 <when value="paired">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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20 <param name="fqinputs" type="data_collection" collection_type="list:paired" label="paired-end reads infile(s)" format="fastqsanger,fastqsanger.gz"/>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
matthias
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21 <param name="barcode_encoding" type="select" label="Barcode location">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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22 <expand macro="barcode_encoding_pair" type="Barcode" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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23 </param>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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24 </when>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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25 </conditional>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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26 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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27 </xml>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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28 <token name="@FASTQ_INPUT_PREPROC@"><![CDATA[
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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29 #for $input in $input_type.fqinputs:
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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30 #if $input_type.options_type_selector == "single"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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31 #set $isfq=$input.is_of_type('fastqsanger')
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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32 #set $name=$clean_ext($input.element_identifier)
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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33 #else:
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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34 #set $isfq=$input.forward.is_of_type('fastqsanger')
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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35 ## TODO if https://github.com/galaxyproject/galaxy/pull/7031 is
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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36 ## backported use element_identifier consistently and fix release in <tool>?
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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37 #set $name=$clean_ext($input.name)
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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38 #end if
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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39
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40 #if $isfq:
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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41 #set $ext = "fastq"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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42 #set inputype = "fastq"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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43 #else
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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44 #set $ext = "fastq.gz"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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45 #set inputype = "gzfastq"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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46 #end if
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47
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48 #if $input_type.options_type_selector == "single"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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49 ln -s '$input' 'stacks_inputs/${name}.${ext}' &&
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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50 #else:
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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51 ## procrad needs _R[12]_ in the file name, so we add an add 0
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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52 ln -s '$input.forward' 'stacks_inputs/${name}_R1_0.${ext}' &&
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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53 ln -s '$input.reverse' 'stacks_inputs/${name}_R2_0.${ext}' &&
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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54 #end if
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55 #end for
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56 ]]></token>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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57 <token name="@PROCESS_IOOPTIONS@"><![CDATA[
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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58 -p stacks_inputs/
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59 #if $input_type.options_type_selector == "paired"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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60 --paired
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61 #end if
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62 -i $inputype
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63 -b '$barcode'
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64 $input_type.barcode_encoding
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65 #if str( $outype ) != "auto"
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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66 -y $outype
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67 #end if
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68 -o stacks_outputs
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69 ]]></token>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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70 <xml name="process_output_types">
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71 <param name="outype" argument="-y" type="select" label="Output format" >
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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72 <option value="auto" selected="True">Same as input</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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73 <option value="fastq">fastq</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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74 <option value="fasta">fasta</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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75 <option value="gzfastq">gzipped fastq</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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76 <option value="gzfasta">gzipped fasta</option>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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77 </param>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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78 </xml>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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79
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80 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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81 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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82 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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83 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" />
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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84 </xml>
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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85 <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
8427e904f352 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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86 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" />
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87 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" />
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88 </xml>
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89
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90 <xml name="process_outputs">
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91 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
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92 <filter>input_type['options_type_selector'] == "single"</filter>
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93 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
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94 </collection>
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95 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
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96 <filter>input_type['options_type_selector'] == "paired"</filter>
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97 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
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98 </collection>
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99
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100 <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
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101 <filter>input_type['options_type_selector'] == "paired"</filter>
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102 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
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103 </collection>
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104
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105 <!-- note irrespective of -y output is always named fastq and are never zipped -->
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106 <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
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107 <filter>capture is True and input_type['options_type_selector'] == "single"</filter>
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108 <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
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109 </collection>
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110 <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads">
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111 <filter>capture is True and input_type['options_type_selector'] == "paired"</filter>
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112 <expand macro="discover_faq_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/discarded"/>
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113 </collection>
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114 </xml>
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115
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116 <!-- FASTQ filtering options -->
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117 <xml name="process_filter">
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118 <conditional name="filter_cond" >
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119 <param name="filter_select" type="select" label="do quality filtering">
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120 <option value="yes">Yes</option>
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121 <option value="no" selected="true">No</option>
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122 </param>
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123 <when value="yes">
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124 <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" />
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125 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" />
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126 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
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127 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
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128 <param argument="--filter_illumina" type="boolean" checked="false" truevalue="--filter_illumina" falsevalue="" label="discard reads that have been marked by Illumina's chastity/purity filter as failing" />
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129 </when>
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130 <when value="no">
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131 <param argument="--len_limit" type="integer" value="" optional="true" label="minimum sequence length" help="useful if your data has already been trimmed"/>
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132 </when>
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133 </conditional>
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134 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
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135 </xml>
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136 <token name="@PROCESS_FILTER@"><![CDATA[
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137 #if $filter_cond.filter_select == 'yes':
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138 -w $filter_cond.sliding
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139 -s $filter_cond.score
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140 $filter_cond.remove
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141 $filter_cond.discard
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142 $filter_cond.filter_illumina
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143 #else
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144 #if str($filter_cond.len_limit) != "":
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145 --len_limit $filter_cond.len_limit
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146 #end if
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147 #end if
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148 $capture
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149 ]]></token>
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150 <token name="@PROCESS_FASTQ_POSTPROC@"><![CDATA[
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151 #if $capture:
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152 && mkdir stacks_outputs/discarded/
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153 && mv stacks_outputs/*discards stacks_outputs/discarded/
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154
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155 ## fix the _R[12]_0 that was added for preparing the input
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156 #if $input_type.options_type_selector == 'paired':
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157 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done
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158 #end if
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159 ## also remove the gz which is added by procrad (but its uncompressed)
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160 && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done
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161
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162 ## the discard files are named fastq even if the output is fasta
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163 #if str($outype).endswith("fasta"):
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164 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done
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165 #else
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166 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done
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167 #end if
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168 #end if
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169 ## prepare paired read output for processing in galaxy
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170 #if $input_type.options_type_selector == 'paired':
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171 && mkdir stacks_outputs/remaining
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172 && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done
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173 && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done
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174 #end if
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175 ]]></token>
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176
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177
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178
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179 <!-- adapter trimming options -->
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180 <xml name="process_adapter">
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181 <param argument="--adapter_1" type="text" value="" optional="true" label="adaptor sequence that may occur on the first read" />
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182 <param argument="--adapter_2" type="text" value="" optional="true" label="adaptor sequence that may occur on the paired-read" />
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183 <param argument="--adapter_mm" type="integer" value="" optional="true" label="number of mismatches allowed in the adapter sequence"/>
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184 </xml>
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185 <token name="@PROCESS_ADAPTER@"><![CDATA[
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186 ## Adapter options
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187 #if str($options_advanced.adapter_1) != "":
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188 --adapter_1 $options_advanced.adapter_1
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189 #end if
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190 #if str($options_advanced.adapter_2) != "":
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191 --adapter_2 $options_advanced.adapter_2
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192 #end if
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193 #if str($options_advanced.adapter_mm) != "":
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194 --adapter_mm $options_advanced.adapter_mm
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195 #end if
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196 ]]></token>
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197
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198 <!-- barcode rescue options -->
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199 <xml name="rescue_barcode">
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200 <conditional name="rescue_cond">
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201 <param name="rescue" type="select" argument="-r" label="Rescue mutated barcodes and RAD-Tags?">
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202 <option value="-r">yes</option>
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203 <option value="" selected="true">no</option>
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204 </param>
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205 <when value="-r">
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206 <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/>
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207 <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/>
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208 </when>
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209 <when value=""/>
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210 </conditional>
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211 </xml>
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212 <token name="@RESCUE_BARCODE@"><![CDATA[
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213 #if str($options_advanced.rescue_cond.rescue) != ""
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214 $options_advanced.rescue_cond.rescue
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215 #if str($options_advanced.rescue_cond.barcode_dist_1) != "":
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216 --barcode_dist_1 $options_advanced.rescue_cond.barcode_dist_1
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217 #end if
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218 #if str($options_advanced.rescue_cond.barcode_dist_2) != "":
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219 --barcode_dist_2 $options_advanced.rescue_cond.barcode_dist_2
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220 #end if
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221 #end if
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222 ]]></token>
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223
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224 <!-- advanced options that are shared -->
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225 <xml name="common_advanced">
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226 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
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227 <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" />
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228 </xml>
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229 <token name="@COMMON_ADVANCED@"><![CDATA[
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230 #if str($options_advanced.truncate)
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231 -t $options_advanced.truncate
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232 #end if
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233 $options_advanced.retain_header
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234 ]]></token>
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235 </macros>