Mercurial > repos > matthias > stacks2_kmerfilter

annotate stacks_kmerfilter.xml @ 7:88031e0bf219 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:56:37 -0400
parents e0b1e96c4032
children
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1 <tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Identify PCR clones</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
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11 mkdir stacks_inputs stacks_outputs &&
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13 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
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14 $link_command
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15
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16 kmer_filter
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17 #if $input_type.input_type_select == 'single':
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18 -f '$fwd_path'
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19 #else
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20 -1 '$fwd_path'
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21 -2 '$rev_path'
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22 #end if
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23 ## TODO $options_kmer_char.read_k_freq
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24 -i $inputype
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25 -o stacks_outputs
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26 $capture
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27 -y fastq
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28 $options_filtering.rare
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29 $options_filtering.abundant
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30 --k_len $options_filtering.k_len
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31 --max_k_freq $options_advanced_filtering.max_k_freq
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32 #if str($options_advanced_filtering.min_lim)!="":
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33 --min_lim $options_advanced_filtering.min_lim
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34 #end if
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35 #if str($options_advanced_filtering.max_lim)!="":
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36 --max_lim $options_advanced_filtering.max_lim
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37 #end if
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38 #if str($options_normalization.normalize)!="":
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39 --normalize $options_normalization.normalize
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40 #end if
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41 #if $options_kmer_char.write_k_freq
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42 --read_k_freq $kfreq
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43 #end if
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44 $options_kmer_char.k_dist
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45 #if $options_kmer_char.k_dist
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46 | sed 's/KmerFrequency/# KmerFrequency/' > $kfreqdist
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47 #end if
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48 @TEE_APPEND_LOG@
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49 @CAT_LOG_TO_STDERR@
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50
5
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51 ## move outputs such that Galaxy can find them
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52 ## if filtering is on then ...filt...fq is created
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53 ## if normalization is on then ...norm...fq is created
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54 ## if both are active then both files are created, but only norm is needed
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55 #if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":
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56 #if str($options_normalization.normalize)!="":
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57 #set infix="norm"
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58 #else
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59 #set infix="fil"
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60 #end if
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61 #if $capture:
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62 #if $input_type.input_type_select == "single"
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63 && mv stacks_outputs/*.discards.fastq '$discarded'
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64 #else
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65 && mv stacks_outputs/*.1.discards.fastq '$discarded_pair.forward'
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66 && mv stacks_outputs/*.2.discards.fastq '$discarded_pair.reverse'
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67 #end if
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68 #end if
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69 #if $input_type.input_type_select == "single"
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70 && mv stacks_outputs/*.${infix}.fastq '$clean'
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71 #else
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72 && mv stacks_outputs/*.1.${infix}.fastq '$clean_pair.forward'
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73 && mv stacks_outputs/*.2.${infix}.fastq '$clean_pair.reverse'
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74 #end if
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75 #end if
0
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76
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77 ]]></command>
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78 <inputs>
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79 <expand macro="fastq_input_bc"/>
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80 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
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81 <section name="options_filtering" title="Filtering options" expanded="False">
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82 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" />
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83 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" />
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84 <param argument="--k_len" type="integer" value="15" label="K-mer size" />
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85 </section>
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86 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">
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87 <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant" />
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88 <param argument="--min_lim" type="integer" value="" optional="true" label="Number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)." />
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89 <param argument="--max_lim" type="integer" value="" optional="true" label="Number of abundant kmers required to discard a read" help="(default: 80% of the k-mers in a read)" />
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90 </section>
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91 <section name="options_normalization" title="Normalization options" expanded="False">
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92 <param argument="--normalize" type="integer" value="" optional="true" label="Normalize read depth according to k-mer coverage" />
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93 </section>
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94 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False">
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95 <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="Write kmers along with their frequency of occurrence and exit" />
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96 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="Print k-mer frequency distribution and exit" />
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97 </section>
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98 <!--<section name="options_advanced_input" title="Advanced input options" expanded="False">
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99 <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="Read a set of kmers along with their frequencies of occurrence instead of reading raw input files" />
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100 </section>-->
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101 <expand macro="in_log"/>
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102 </inputs>
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103 <outputs>
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104 <expand macro="out_log"/>
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105 <data name="clean" format="fastqsanger" label="${tool.name} on ${on_string}">
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106 <filter>input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
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107 </data>
5
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108 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
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109 <filter>input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
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110 </collection>
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111 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
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112 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
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113 </data>
5
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114 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
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115 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
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116 </collection>
3
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117 <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
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118 <filter>options_kmer_char['write_k_freq']</filter>
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119 </data>
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120 <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution">
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121 <filter>options_kmer_char['k_dist']</filter>
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122 </data>
0
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123 </outputs>
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124 <tests>
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125 <!-- default output for filtering -->
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126 <test>
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127 <conditional name="input_type">
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128 <param name="input_type_select" value="single" />
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129 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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130 </conditional>
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131 <param name="add_log" value="yes" />
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132 <output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/>
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133 <param name="rare" value="--rare"/>
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134 <param name="abundant" value="--abundant" />
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135 <param name="k_len" value="16" />
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136 <assert_command>
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137 <has_text text="--rare" />
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138 <has_text text="--abundant" />
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139 <has_text text="--k_len 16" />
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140 </assert_command>
0
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141 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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142 </test>
3
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143 <test>
5
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144 <conditional name="input_type">
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145 <param name="input_type_select" value="paired" />
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146 <param name="fqinputs">
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147 <collection type="paired">
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148 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
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149 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
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150 </collection>
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151 </param>
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152 </conditional>
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153 <param name="capture" value="-D" />
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154 <param name="normalize" value="1" />
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155 <assert_command>
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156 <has_text text="--normalize 1" />
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157 </assert_command>
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158 <output_collection name="clean_pair" type="paired">
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159 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
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160 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
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161 </output_collection>
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162 <output_collection name="discarded_pair" type="paired">
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163 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
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164 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
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165 </output_collection>
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166 </test>
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167 <!-- kfreq output -->
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168 <test>
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169 <conditional name="input_type">
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170 <param name="input_type_select" value="single" />
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171 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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172 </conditional>
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173 <section name="options_kmer_char">
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174 <param name="write_k_freq" value="--write_k_freq" />
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175 </section>
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176 <output name="kfreq" file="kmerfilter/kfreq.tsv"/>
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177 </test>
5
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178 <!-- kfreqdist output -->
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179 <test>
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180 <conditional name="input_type">
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181 <param name="input_type_select" value="single" />
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182 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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183 </conditional>
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184 <section name="options_kmer_char">
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185 <param name="k_dist" value="--k_dist" />
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186 </section>
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187 <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>
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188 </test>
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189 </tests>
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190 <help>
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191 <![CDATA[
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192 .. class:: infomark
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193
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194 Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.
0
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195
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196 @STACKS_INFOS@
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197 ]]>
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198 </help>
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199 <expand macro="citation" />
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200 </tool>