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annotate kat_filter.xml @ 0:894eff01255b draft default tip

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planemo upload commit 3ad4270aabe37123987e91a178bd7d61778c849c-dirty
author nml
date Tue, 09 Jan 2018 10:27:22 -0500
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
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3 <description>Filtering reads or k-mer from fasta file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">filter_seq</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12
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13
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14 cp "$db" db.fasta &&
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15
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16 #if $single_or_paired.type == "single"
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17 ln "$input_se" read.fastq &&
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18
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19 kat filter seq
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20
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21 --seq read.fastq
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22
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23 #elif $single_or_paired.type == "paired"
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24 ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
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25
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26 kat filter seq
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27
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28 --seq read_1.fastq --seq2 read_2.fastq
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29
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30 #else
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31 ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
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32
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33 kat filter seq
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34
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35 --seq read_1.fastq --seq2 read_2.fastq
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36
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37 #end if
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38
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39
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40 @THREADS@
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41
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42 --mer_len $kmer
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43
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44 $stats
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45
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46 #if $invert_or_both.which == "invert":
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47 $invert_or_both.invert
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48 #elif $invert_or_both.which == "split":
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49 $invert_or_both.separate
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50 #end if
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51
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52 -o reads
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53 'db.fasta'
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54
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55 ]]></command>
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56 <inputs>
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57 <expand macro="macro_input" />
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58
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59 <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
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60 <expand macro="macro_kmers" />
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61
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62 <param name="threshold" type="float" value='0.10000000000000001' label="Target Threshold" help="What percentage of the sequence needs to be covered with target k-mers to keep the sequence"/>
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63
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64 <param name="stats" type="boolean" truevalue='--stats' falsevalue='' checked='False' label="Stats" help="Whether to emit statistics about quantity of found k-mers in each sequence."/>
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65 <conditional name="invert_or_both">
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66 <param name="which" type="select" label="Advance Options">
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67 <option value="none">No Advance</option>
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68 <option value="invert">Option 1</option>
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69 <option value="split">Option 2</option>
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70 </param>
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71 <when value="invert">
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72 <param name="invert" type="boolean" truevalue='--invert' falsevalue='' checked='True' label="Take k-mer not matching target" help="Whether to take k-mers outside region as selected content, rather than those inside."/>
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73 </when>
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74 <when value="split">
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75 <param name="separate" type="boolean" truevalue='--separate' falsevalue='' checked='True' label="Keep inside and outside of target(s) region" help="Whether to partition the k-mers into two sets, those inside region and those outside."/>
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76 </when>
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77 <when value="none">
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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <data format="fastqsanger" name="reads" label="Reads.fastq" from_work_dir="reads.in.fastq" >
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83 <filter> single_or_paired['type'] == "single" </filter>
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84 </data>
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85 <data format="fastqsanger" name="forward" label="forward_R1.fastq" from_work_dir="reads.in.R1.fastq" >
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86 <filter> single_or_paired['type'] == "paired"</filter>
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87 </data>
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88 <data format="fastqsanger" name="reverse" label="reverse_R2.fastq" from_work_dir="reads.in.R2.fastq" >
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89 <filter> single_or_paired['type'] == "paired"</filter>
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90 </data>
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91
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92
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93 <collection name="paired_reads" type="paired" label="Reads">
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94 <data name="forward" format="fastqsanger" from_work_dir="reads.in.R1.fastq" >
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95 <filter> single_or_paired['type'] == "collection"</filter>
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96 </data>
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97 <data name="reverse" format="fastqsanger" from_work_dir="reads.in.R2.fastq" >
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98 <filter> single_or_paired['type'] == "collection"</filter>
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99 </data>
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100 </collection>
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101
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102
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103 <data format="fastqsanger" name="outside_reads" label='Outside reads' from_work_dir="reads.out.fastq">
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104 <filter>invert_or_both['which'] == 'split' and invert_or_both['separate'] and single_or_paired['type'] == "single"</filter>
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105 </data>
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106 <data format="tabular" name="file_stats" label='Stats' from_work_dir="reads.stats">
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107 <filter>stats</filter>
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108 </data>
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109
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="input_se" value="input.fastq" />
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114 <param name="db" value="db.fasta" />
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115 <output file="matched.fastq" ftype="fastqsanger" name="reads" />
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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119 http://kat.readthedocs.io/en/latest/using.html#filtering-tools
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120 ]]>
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121
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122 </help>
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123 <citations>
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124 </citations>
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125 </tool>