annotate stacks_clonefilter.xml @ 0:a8a0cd05d47d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author iuc
date Sun, 21 May 2017 18:54:11 -0400
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a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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1 <tool id="stacks_clonefilter" name="Stacks: clone filter" version="@WRAPPER_VERSION@.0">
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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2 <description>Identify PCR clones</description>
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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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 <command><![CDATA[
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9
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10 #if $data_type.dt_select == "single"
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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 &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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21 #else
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22
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23 #if $data_type.fwd.is_of_type('fastqsanger')
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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24 #set $ext = ".fq"
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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25 #set inputype = "fastq"
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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26 #else
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27 #set $ext = ".fq.gz"
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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28 #set inputype = "gzfastq"
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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29 #end if
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31 ln -s '$data_type.fwd' R1$ext &&
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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32 ln -s '$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 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 $data_type.dt_select == 'single':
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42 -f R1$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
a8a0cd05d47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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50
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51 -o clone_outputs
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52
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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 $data_type.barcode_encoding
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57 #end if
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58 #if $oligo_len_2
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59 --oligo_len_2 $oligo_len_2
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60 #end if
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61
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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_pair" type="select" label="Barcode location">
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82 <expand macro="barcode_encoding_single" />
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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="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/>
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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
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89 </inputs>
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90 <outputs>
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91 <data format="fastqsangergz" name="clean" from_work_dir="clone_outputs/R1.fq.gz">
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92 <filter>data_type['dt_select'] == 'single'</filter>
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93 </data>
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94
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95 <data format="fastqsangergz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz">
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96 <filter>data_type['dt_select'] == 'pair'</filter>
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97 </data>
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98 <data format="fastqsangergz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz">
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99 <filter>data_type['dt_select'] == 'pair'</filter>
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100 </data>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <conditional name="data_type">
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105 <param name="dt_select" value="single" />
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106 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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107 </conditional>
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108 <param name="oligo_len_1" value="6" />
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109 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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110 </test>
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111 <test>
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112 <conditional name="data_type">
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113 <param name="dt_select" value="single" />
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114 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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115 </conditional>
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116 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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117 </test>
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118 <test>
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119 <conditional name="data_type">
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120 <param name="dt_select" value="pair" />
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121 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
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122 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
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123 </conditional>
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124 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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125 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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126 </test>
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127 <test>
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128 <conditional name="data_type">
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129 <param name="dt_select" value="pair" />
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130 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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131 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
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132 </conditional>
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133 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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134 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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135 </test>
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136 </tests>
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137 <help>
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138 <![CDATA[
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139 .. class:: infomark
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140
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141
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142 The clone_filter program is designed to identify PCR clones.
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143
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144 @STACKS_INFOS@
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145 ]]>
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146 </help>
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147 <expand macro="citation" />
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148 </tool>