Mercurial > repos > matthias > stacks2_clonefilter

annotate stacks_clonefilter.xml @ 3:4758a347d62e 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 13:06:09 -0500
parents 223e7778451a
children c4ed7dacee9b
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1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" version="@STACKS_VERSION@+galaxy@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 #if $data_type.dt_select == "single"
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11
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12 #if $data_type.fname.is_of_type('fastqsanger')
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13 #set $ext = ".fq"
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14 #set inputype = "fastq"
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15 #else
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16 #set $ext = ".fq.gz"
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17 #set inputype = "gzfastq"
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18 #end if
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19
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20 ln -s '$data_type.fname' R1$ext &&
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21 #else
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23 #if $data_type.fwd.is_of_type('fastqsanger')
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24 #set $ext = ".fq"
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25 #set inputype = "fastq"
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26 #else
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27 #set $ext = ".fq.gz"
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28 #set inputype = "gzfastq"
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29 #end if
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30
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31 ln -s '$data_type.fwd' R1$ext &&
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32 ln -s '$data_type.rev' R2$ext &&
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33 #end if
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34
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35
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36 mkdir outputs
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38 &&
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39
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40 clone_filter
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41 #if $data_type.dt_select == 'single':
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42 -f R1$ext
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43 #else
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44 -1 R1$ext
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45 -2 R2$ext
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46 #end if
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47
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48 -i $inputype
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49
3
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50 -o outputs
0
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51 $capture
3
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52 $data_type.barcode_encoding
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53 #if $oligo_len_1
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54 --oligo_len_1 $oligo_len_1
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55 #end if
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56 #if $oligo_len_2
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57 --oligo_len_2 $oligo_len_2
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58 #end if
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59 $retain_oligo
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60 ## only supports fastq.gz output since the
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61 ## the program outputs empty files for fasta/fastq
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62 -y gzfastq
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63 ]]></command>
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64 <inputs>
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65 <conditional name="data_type">
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66 <param name="dt_select" type="select" label="Single or Paired-end">
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67 <option value="single">Single</option>
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68 <option value="pair">Pair</option>
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69 </param>
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70 <when value="single">
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71 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
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72 <param name="barcode_encoding" type="select" label="Barcode location">
3
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73 <expand macro="barcode_encoding_single" type="Random oligo"/>
0
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74 </param>
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75
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76 </when>
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77 <when value="pair">
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78 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
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79 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
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80 <param name="barcode_encoding" type="select" label="Barcode location">
3
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81 <expand macro="barcode_encoding_pair" type="Random oligo"/>
0
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82 </param>
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83 </when>
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84 </conditional>
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85 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
3
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86 <param name="oligo_len_1" type="integer" value="0" label="length of the single-end oligo sequence in data set"/>
0
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87 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/>
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88 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" />
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89
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90 </inputs>
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91 <outputs>
3
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92 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
0
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93 <filter>data_type['dt_select'] == 'single'</filter>
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94 </data>
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95
3
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96 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
0
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97 <filter>data_type['dt_select'] == 'pair'</filter>
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98 </data>
3
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99 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
0
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100 <filter>data_type['dt_select'] == 'pair'</filter>
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101 </data>
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102 </outputs>
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103 <tests>
3
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104 <!-- single end, defaults-->
0
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105 <test>
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106 <conditional name="data_type">
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107 <param name="dt_select" value="single" />
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108 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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109 </conditional>
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110 <param name="oligo_len_1" value="6" />
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111 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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112 </test>
3
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113 <!-- single end, alt BCencoding, capture-->
0
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114 <test>
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115 <conditional name="data_type">
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116 <param name="dt_select" value="single" />
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117 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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118 <param name="barcode_encoding" value="--index_null" />
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119 </conditional>
3
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120 <param name="capture" value="-D" />
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121 <param name="oligo_len_1" value="6" />
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122 <assert_command>
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123 <has_text text="-D" />
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124 </assert_command>
0
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125 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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126 </test>
3
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127 <!-- paired end, defaults-->
0
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128 <test>
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129 <conditional name="data_type">
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130 <param name="dt_select" value="pair" />
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131 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
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132 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
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133 </conditional>
3
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134 <param name="oligo_len_1" value="6" />
0
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135 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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136 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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137 </test>
3
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138 <!-- paired end, non defaults-->
0
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139 <test>
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140 <conditional name="data_type">
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141 <param name="dt_select" value="pair" />
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142 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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143 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
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144 </conditional>
3
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145 <param name="oligo_len_1" value="6" />
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146 <param name="capture" value="-D" />
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147 <param name="retain_oligo" value="--retain_oligo" />
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148 <assert_command>
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149 <has_text text="--retain_oligo" />
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150 </assert_command>
0
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151 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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152 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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153 </test>
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154 </tests>
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155 <help>
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156 <![CDATA[
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157 .. class:: infomark
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158
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159 The clone_filter program is designed to identify PCR clones.
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160
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161 @STACKS_INFOS@
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162 ]]>
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163 </help>
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164 <expand macro="citation" />
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165 </tool>