Mercurial > repos > matthias > stacks2_kmerfilter

annotate stacks_kmerfilter.xml @ 1:36b792bf9dd6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Thu, 29 Nov 2018 12:17:07 -0500
parents ef1485568631
children 324a729c257f
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36b792bf9dd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
matthias
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1 <tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" version="@WRAPPER_VERSION@">
0
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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="stdio"/>
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8 <expand macro="version_cmd"/>
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9 <command><![CDATA[
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10
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11 #if $data_type.dt_select == "single"
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12
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13 #if $data_type.fname.is_of_type('fastqsanger')
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14 #set $ext = ".fq"
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15 #set inputype = "fastq"
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16 #else
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17 #set $ext = ".fq.gz"
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18 #set inputype = "gzfastq"
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19 #end if
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21 ln -s '$data_type.fname' R1$ext &&
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22 #else
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24 #if $data_type.fwd.is_of_type('fastqsanger')
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25 #set $ext = ".fq"
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26 #set inputype = "fastq"
ef1485568631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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27 #else
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28 #set $ext = ".fq.gz"
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29 #set inputype = "gzfastq"
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30 #end if
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31
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32 ln -s '$data_type.fwd' R1$ext &&
ef1485568631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 ln -s '$data_type.rev' R2$ext &&
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34 #end if
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35
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36 mkdir clone_outputs
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37
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38 &&
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39
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40 clone_filter
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41 #if $data_type.dt_select == 'single':
ef1485568631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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42 -f R1$ext
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43
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44 #else
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45 -1 R1$ext
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46 -2 R2$ext
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47 #end if
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48
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49 -i $inputype
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50
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51 -o clone_outputs
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52 $capture
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53
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54 #if $oligo_len_1
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55 --oligo_len_1 $oligo_len_1
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56 #end if
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57 #if $oligo_len_2
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58 --oligo_len_2 $oligo_len_2
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59 #end if
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60 $data_type.barcode_encoding
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61 $retain_oligo
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62 -y gzfastq
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63
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64 ]]></command>
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65 <inputs>
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66 <conditional name="data_type">
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67 <param name="dt_select" type="select" label="Single or Paired-end">
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68 <option value="single">Single</option>
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69 <option value="pair">Pair</option>
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70 </param>
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71 <when value="single">
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72 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
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73 <param name="barcode_encoding" type="select" label="Barcode location">
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74 <expand macro="barcode_encoding_single" />
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75 </param>
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76
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77 </when>
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78 <when value="pair">
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79 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
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80 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
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81 <param name="barcode_encoding" type="select" label="Barcode location">
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82 <expand macro="barcode_encoding_pair" />
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83 </param>
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84 </when>
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85 </conditional>
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86 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
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87 <section name="options_filtering" title="Filtering options" expanded="False">
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88 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="turn on filtering based on rare k-mers" />
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89 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="turn on filtering based on abundant k-mers" />
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90 <param argument="--k_len" type="integer" value="15" label="k-mer size" />
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91 </section>
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92 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">
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93 </section>
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94 <param argument="--max_k_freq" type="integer" value="20" label="number of times a kmer must occur to be considered abundant" />
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95 <param argument="--min_lim" type="integer" value="" optional="true" label="number of rare kmers occuring in a row required to discard a read" help="(0/empty: 80% of the k-mer length)." />
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96 <param argument="--max_lim" type="integer" value="" optional="true" label="number of abundant kmers required to discard a read" help="(0/empty: 80% of the k-mers in a read)" />
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97 <section name="options_normalization" title="Normalization options" expanded="False">
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98 <param argument="--normalize" type="integer" value="" label="normalize read depth according to k-mer coverage" />
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99 </section>
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100 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False">
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101 <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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102 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="print k-mer frequency distribution and exit" />
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103 </section>
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104 <section name="options_advanced_input" title="Advanced input options" expanded="False">
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105 <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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106 </section>
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107 </inputs>
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108 <outputs>
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109 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
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110 <filter>data_type['dt_select'] == 'single'</filter>
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111 </data>
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112
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113 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
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114 <filter>data_type['dt_select'] == 'pair'</filter>
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115 </data>
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116 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
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117 <filter>data_type['dt_select'] == 'pair'</filter>
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118 </data>
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119 </outputs>
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120 <tests>
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121 <test>
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122 <conditional name="data_type">
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123 <param name="dt_select" value="single" />
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124 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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125 </conditional>
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126 <param name="oligo_len_1" value="6" />
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127 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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128 </test>
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129 <!--<test>
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130 <conditional name="data_type">
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131 <param name="dt_select" value="single" />
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132 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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133 <param name="barcode_encoding" value="\-\-inline_null" />
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134
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135 </conditional>
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136 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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137 </test>
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138 <test>
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139 <conditional name="data_type">
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140 <param name="dt_select" value="pair" />
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141 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
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142 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
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143 </conditional>
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144 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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145 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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146 </test>
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147 <test>
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148 <conditional name="data_type">
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149 <param name="dt_select" value="pair" />
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150 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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151 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
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152 </conditional>
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153 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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154 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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155 </test>-->
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156 </tests>
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157 <help>
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158 <![CDATA[
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159 .. class:: infomark
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160
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161 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.
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162
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163 @STACKS_INFOS@
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164 ]]>
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165 </help>
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166 <expand macro="citation" />
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167 </tool>