Mercurial > repos > matthias > stacks2_clonefilter

annotate stacks_clonefilter.xml @ 7:e9295ac66416 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 Wed, 26 Jun 2019 05:17:17 -0400
parents b707e9def9ff
children
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1 <tool id="stacks2_clonefilter" name="Stacks2: clone 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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16 clone_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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24 -i $inputype
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26 -o stacks_outputs
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27 $capture
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28 $input_type.barcode_encoding
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29 #if $oligo_len_1
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30 --oligo_len_1 $oligo_len_1
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31 #end if
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32 #if $oligo_len_2
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33 --oligo_len_2 $oligo_len_2
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34 #end if
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35 $retain_oligo
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36 ## only supports fastq.gz output since the
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37 ## the program outputs empty files for fasta/fastq
c4ed7dacee9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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38 -y gzfastq
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39 @TEE_APPEND_LOG@
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40 @CAT_LOG_TO_STDERR@
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41
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42 ## move outputs such that Galaxy can find them
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43 #if $capture:
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44 #if $input_type.input_type_select == "single"
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45 && mv stacks_outputs/*.discards.fq.gz '$discarded'
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46 #else
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47 && mv stacks_outputs/*.discards.1.fq.gz '$discarded_pair.forward'
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48 && mv stacks_outputs/*.discards.2.fq.gz '$discarded_pair.reverse'
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49 #end if
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50 #end if
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51 #if $input_type.input_type_select == "single"
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52 && mv stacks_outputs/*.fq.gz '$clean'
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53 #else
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54 && mv stacks_outputs/*.1.fq.gz '$clean_pair.forward'
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55 && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse'
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56 #end if
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57 ]]></command>
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58 <inputs>
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59 <expand macro="fastq_input_bc"/>
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60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
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61 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
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62 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
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63 <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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64 <expand macro="in_log"/>
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65 </inputs>
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66 <outputs>
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67 <expand macro="out_log"/>
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68 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
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69 <filter>input_type['input_type_select'] == 'single'</filter>
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70 </data>
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71 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
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72 <filter>input_type['input_type_select'] == 'paired'</filter>
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73 </collection>
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74 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
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75 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
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76 </data>
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77 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
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78 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
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79 </collection>
0
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80 </outputs>
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81 <tests>
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82 <!-- single end, defaults-->
0
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83 <test>
5
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84 <conditional name="input_type">
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85 <param name="input_type_select" value="single" />
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86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
0
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87 </conditional>
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88 <param name="oligo_len_1" value="6" />
6
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89 <param name="add_log" value="yes" />
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90 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
0
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91 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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92 </test>
3
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93 <!-- single end, alt BCencoding, capture-->
0
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94 <test>
5
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95 <conditional name="input_type">
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96 <param name="input_type_select" value="single" />
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97 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
0
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98 <param name="barcode_encoding" value="--index_null" />
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99 </conditional>
3
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100 <param name="capture" value="-D" />
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101 <param name="oligo_len_1" value="6" />
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102 <assert_command>
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103 <has_text text="-D" />
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104 </assert_command>
0
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105 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
5
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106 <output name="discarded" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
0
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107 </test>
3
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108 <!-- paired end, defaults-->
0
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109 <test>
5
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110 <conditional name="input_type">
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111 <param name="input_type_select" value="paired" />
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112 <param name="fqinputs">
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113 <collection type="paired">
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114 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
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115 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
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116 </collection>
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117 </param>
0
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118 </conditional>
3
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119 <param name="oligo_len_1" value="6" />
5
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120 <output_collection name="clean_pair" type="paired">
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121 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
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122 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
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123 </output_collection>
0
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124 </test>
5
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125 <!-- paired end, non defaults -->
0
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126 <test>
5
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127 <conditional name="input_type">
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128 <param name="input_type_select" value="paired" />
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129 <param name="fqinputs">
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130 <collection type="paired">
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131 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
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132 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
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133 </collection>
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134 </param>
0
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135 </conditional>
3
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136 <param name="oligo_len_1" value="6" />
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137 <param name="capture" value="-D" />
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138 <param name="retain_oligo" value="--retain_oligo" />
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139 <assert_command>
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140 <has_text text="--retain_oligo" />
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141 </assert_command>
5
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142 <output_collection name="clean_pair" type="paired">
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143 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
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144 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
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145 </output_collection>
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146 <output_collection name="discarded_pair" type="paired">
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147 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
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148 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
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149 </output_collection>
0
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150 </test>
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151 </tests>
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152 <help>
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153 <![CDATA[
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154 .. class:: infomark
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155
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156 The clone_filter program is designed to identify PCR clones.
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157
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158 @STACKS_INFOS@
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159 ]]>
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160 </help>
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161 <expand macro="citation" />
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162 </tool>