annotate stacks_procrad.xml @ 5:b4bab607eb05 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:31:20 +0000
parents bd5ff77e2036
children
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5
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1 <tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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2 <description>the Stacks demultiplexing script</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_process.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_cmd"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @FASTQ_INPUT_FUNCTIONS@
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11
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12 #if $input_type.barcode_encoding != ''
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13 python '$__tool_directory__'/check_bcfile.py '$input_type.barcode' &&
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14 #end if
0
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15 mkdir stacks_inputs stacks_outputs &&
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16
1
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17 #if $output_log
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18 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log &&
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19 #end if
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20
0
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21 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
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22 $link_command
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24 process_radtags
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25
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26 @PROCESS_IOOPTIONS@
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27 @PROCESS_FILTER@
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28 @COMMON_ADVANCED@
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29 @RESCUE_BARCODE@
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30 @PROCESS_ADAPTER@
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31
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32 ## -E not implemented in Galaxy defaults to phred33
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33
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34 ## Restriction enzyme options
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35 #if str($options_enzyme.enzyme) != '':
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36 -e $options_enzyme.enzyme
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37 #end if
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38 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='':
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39 --renz_2 $options_enzyme.enzyme2
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40 #end if
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41
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42 ## advanced options not shared between shortreads and radtags
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43 $options_advanced.bestrad
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44 $options_advanced.disable_rad_check
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45
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46 ## Output options
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47 ## --merge not implemented in Galaxy
1
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48
0
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49 @PROCESS_FASTQ_POSTPROC@
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50 ]]></command>
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51
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52 <inputs>
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53 <conditional name="input_type">
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54 <param name="input_type_select" type="select" label="Single-end or paired-end reads">
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55 <option value="single" selected="True">Single-end files</option>
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56 <option value="paired">Paired-end files</option>
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57 </param>
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58 <when value="single">
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59 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Singles-end reads"/>
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60 <expand macro="barcode_selector">
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61 <expand macro="barcode_encoding_single" type="Barcode"/>
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62 </expand>
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63 </when>
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64 <when value="paired">
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65 <param name="fqinputs" type="data_collection" collection_type="list:paired" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/>
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66 <expand macro="barcode_selector">
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67 <expand macro="barcode_encoding_pair" type="Barcode"/>
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68 </expand>
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69 </when>
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70 </conditional>
0
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71 <conditional name="options_enzyme">
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72 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
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73 <option value="1">One</option>
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74 <option value="2">Two</option>
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75 </param>
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76 <when value="1">
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77 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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78 <expand macro="enzymes"/>
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79 </param>
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80 </when>
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81 <when value="2">
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82 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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83 <expand macro="enzymes"/>
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84 </param>
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85 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
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86 <expand macro="enzymes"/>
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87 </param>
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88 </when>
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89 </conditional>
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90
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91 <section name="options_advanced" title="advanced options" expanded="False">
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92 <expand macro="common_advanced"/>
2
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93 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/>
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94 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/>
0
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95 <expand macro="rescue_barcode"/>
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96 <expand macro="process_adapter"/>
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97 </section>
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98
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99 <expand macro="process_filter"/>
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100 <expand macro="process_output_types"/>
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101 <expand macro="in_log"/>
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102 </inputs>
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103
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104 <outputs>
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105 <expand macro="out_log"/>
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106 <expand macro="process_outputs">
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107 <collection name="processed" type="list" label="${tool.name} on ${on_string} Processed reads">
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108 <filter>input_type['input_type_select'] == "single"</filter>
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109 <filter>input_type['barcode_encoding'] == ""</filter>
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110 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
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111 </collection>
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112 <collection name="processed_paired" type="list:paired" label="${tool.name} on ${on_string} Processed reads">
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113 <filter>input_type['input_type_select'] == "paired"</filter>
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114 <filter>input_type['barcode_encoding'] == ""</filter>
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115 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
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116 </collection>
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117 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
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118 <filter>input_type['input_type_select'] == "single"</filter>
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119 <filter>input_type['barcode_encoding'] != ""</filter>
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120 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
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121 </collection>
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122 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
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123 <filter>input_type['input_type_select'] == "paired"</filter>
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124 <filter>input_type['barcode_encoding'] != ""</filter>
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125 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
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126 </collection>
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127 </expand>
0
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128 </outputs>
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129 <tests>
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130 <!-- 01 single single ended input, no filtering (hence no capturing) + log -->
2
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131 <test expect_num_outputs="2">
0
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132 <param name="input_type|input_type_select" value="single"/>
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133 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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134 <param name="input_type|barcode_encoding" value="--inline_null"/>
5
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135 <param name="input_type|barcode" value="procrad/barcodes"/>
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136 <param name="options_enzyme|options_enzyme_selector" value="1"/>
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137 <param name="options_enzyme|enzyme" value="ecoRI"/>
2
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138 <param name="add_log" value="yes"/>
0
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139 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/>
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140 <output_collection name="demultiplexed" count="40">
5
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141 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" compare="contains"/>
0
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142 </output_collection>
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143 </test>
5
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144 <!-- 02 multiple (zipped) single end input (misusing R2 as add single end read file),
0
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145 discarding by quality and capturing them -->
2
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146 <test expect_num_outputs="3">
0
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147 <param name="input_type|input_type_select" value="single"/>
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148 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/>
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149 <param name="input_type|barcode_encoding" value="--inline_null"/>
5
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150 <param name="input_type|barcode" value="procrad/barcodes"/>
0
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151 <param name="options_enzyme|options_enzyme_selector" value="1"/>
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152 <param name="options_enzyme|enzyme" value="ecoRI"/>
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153 <param name="filter_cond|filter_select" value="yes"/>
1
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154 <param name="filter_cond|discard" value="-q"/>
2
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155 <param name="filter_cond|sliding" value="0.1"/>
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156 <param name="filter_cond|score" value="11"/>
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157 <param name="filter_cond|remove" value="-c"/>
1
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158 <param name="capture" value="-D"/>
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159 <param name="outype" value="gzfastq"/>
2
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160 <param name="add_log" value="yes"/>
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161 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/>
0
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162 <assert_command>
2
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163 <has_text text="-q"/>
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164 <has_text text="-w 0.1"/>
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165 <has_text text="-s 11"/>
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166 <has_text text="-c"/>
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167 <has_text text="-D"/>
0
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168 </assert_command>
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169 <output_collection name="demultiplexed" count="40">
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170 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
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171 </output_collection>
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172 <output_collection name="discarded" count="2">
5
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173 <element name="R1">
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174 <assert_contents>
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175 <has_size value="1101516" delta="200"/>
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176 <has_text text="@lane1_fakedata0_11 1:N:0:"/>
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177 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
178 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
179 <element name="R2">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
180 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
181 <has_size value="1613724" delta="200"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
182 <has_text text="@lane1_fakedata0_0 1:N:0:"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
183 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
184 </element>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
185 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
186 </test>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
187 <!-- 03 paired input, no quality but length filter, gzfasta output -->
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
188 <test expect_num_outputs="4">
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
189 <param name="input_type|input_type_select" value="paired"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
190 <param name="input_type|fqinputs">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
191 <collection type="list:paired">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
192 <element name="reads">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
193 <collection type="paired">
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
194 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
195 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
196 </collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
197 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
198 </collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
199 </param>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
200 <param name="input_type|barcode" value="procrad/barcodes"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
201 <param name="options_enzyme|options_enzyme_selector" value="1"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
202 <param name="options_enzyme|enzyme" value="ecoRI"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
203 <param name="filter_cond|filter_select" value="no"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
204 <param name="filter_cond|len_limit" value="50"/>
1
ca7aa77c7f57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
205 <param name="capture" value="-D"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
206 <param name="outype" value="gzfasta"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
207 <param name="add_log" value="yes"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
208 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
209 <assert_command>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
210 <has_text text="--len_limit 50"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
211 </assert_command>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
212 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
213 <element name="PopA_01">
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
214 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
215 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
216 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
217 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
218 <output_collection name="remaining" type="list:paired" count="40">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
219 <element name="PopA_01">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
220 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
221 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa.gz" ftype="fasta.gz"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
222 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
223 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
224 <output_collection name="discarded_paired" type="list:paired" count="1">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
225 <element name="reads">
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
226 <element name="forward">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
227 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
228 <has_size value="609382" delta="200"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
229 <has_text text=">lane1_fakedata0_11 1:N:0:"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
230 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
231 </element>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
232 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
233 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
234 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
235 </test>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
236 <!-- 04 paired input (gzipped) + advanced options + two enzymes, fasta output -->
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
237 <test expect_num_outputs="3">
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
238 <param name="input_type|input_type_select" value="paired"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
239 <param name="input_type|fqinputs">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
240 <collection type="list:paired">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
241 <element name="reads">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
242 <collection type="paired">
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
243 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
244 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
245 </collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
246 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
247 </collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
248 </param>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
249 <param name="input_type|barcode" value="procrad/barcodes"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
250 <param name="options_enzyme|options_enzyme_selector" value="2"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
251 <param name="options_enzyme|enzyme" value="ecoRI"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
252 <param name="options_enzyme|enzyme2" value="ecoRI"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
253 <param name="options_advanced|truncate" value="70"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
254 <param name="options_advanced|rescue_cond|rescue" value="-r"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
255 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
256 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
257 <param name="options_advanced|bestrad" value="--bestrad"/>
1
ca7aa77c7f57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
258 <param name="options_advanced|retain_header" value="--retain_header"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
259 <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
260 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
261 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
262 <param name="options_advanced|adapter_mm" value="2"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
263 <param name="outype" value="fasta"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
264 <assert_command>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
265 <has_text text="-e ecoRI"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
266 <has_text text="--renz_2 ecoRI"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
267 <has_text text="-t 70"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
268 <has_text text="-r"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
269 <has_text text="--bestrad"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
270 <has_text text="--retain_header"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
271 <has_text text="--disable_rad_check"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
272 <has_text text="--barcode_dist_1 2"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
273 <has_text text="--barcode_dist_2 2"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
274 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
275 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
276 <has_text text="--adapter_mm 2"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
277 </assert_command>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
278 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
279 <element name="PopA_01">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
280 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
281 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
282 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
283 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
284 <output_collection name="remaining" type="list:paired" count="40">
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
285 <element name="PopA_01">
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
286 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
287 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
288 </element>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
289 </output_collection>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
290 </test>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
291 <!-- 05 test invalid barcode file -->
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
292 <test expect_failure="true">
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
293 <param name="input_type|input_type_select" value="single"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
294 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
295 <param name="input_type|barcode_encoding" value="--inline_null"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
296 <param name="input_type|barcode" value="procrad/barcodes-duplicate"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
297 <param name="options_enzyme|options_enzyme_selector" value="1"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
298 <param name="options_enzyme|enzyme" value="ecoRI"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
299 <param name="add_log" value="yes"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
300 </test>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
301 <!-- 06 test invalid barcode file -->
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
302 <test expect_failure="true">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
303 <param name="input_type|input_type_select" value="single"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
304 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
305 <param name="input_type|barcode_encoding" value="--inline_null"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
306 <param name="input_type|barcode" value="procrad/barcodes-duplicate2"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
307 <param name="options_enzyme|options_enzyme_selector" value="1"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
308 <param name="options_enzyme|enzyme" value="ecoRI"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
309 <param name="add_log" value="yes"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
310 </test>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
311 <!-- 07 test no provided barcode file single-->
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
312 <test expect_num_outputs="3">
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
313 <param name="input_type|input_type_select" value="single"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
314 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
315 <param name="input_type|barcode_encoding" value=""/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
316 <param name="options_enzyme|options_enzyme_selector" value="1"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
317 <param name="options_enzyme|enzyme" value="ecoRI"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
318 <param name="add_log" value="yes"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
319 <param name="capture" value="-D"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
320 <output name="output_log">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
321 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
322 <has_text text="Barcode Not Found"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
323 <has_text text="Retained Reads"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
324 <has_n_lines n="10"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
325 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
326 </output>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
327 <output_collection name="processed" count="1">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
328 <element name="R1">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
329 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
330 <has_size value="20"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
331 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
332 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
333 </output_collection>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
334 <output_collection name="discarded" count="1">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
335 <element name="R1">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
336 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
337 <has_size value="1613724" delta="200"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
338 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
339 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
340 </output_collection>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
341 </test>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
342 <!-- 08 test no provided barcode file paired -->
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
343 <test expect_num_outputs="3">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
344 <param name="input_type|input_type_select" value="paired"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
345 <param name="input_type|fqinputs">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
346 <collection type="list:paired">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
347 <element name="reads">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
348 <collection type="paired">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
349 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
350 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
351 </collection>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
352 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
353 </collection>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
354 </param>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
355 <param name="input_type|barcode_encoding" value=""/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
356 <param name="options_enzyme|options_enzyme_selector" value="1"/>
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
357 <param name="options_enzyme|enzyme" value="ecoRI"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
358 <param name="outype" value="gzfasta"/>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
359 <param name="add_log" value="yes"/>
5
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
360 <output name="output_log" file="procrad/process_radtags_paired_no_barcode.out" lines_diff="4"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
361 <output_collection name="processed_paired" type="list:paired" count="2">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
362 <element name="reads_R1_0">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
363 <element name="forward">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
364 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
365 <has_size value="20"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
366 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
367 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
368 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
369 <element name="reads_R2_0">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
370 <element name="reverse">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
371 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
372 <has_size value="20"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
373 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
374 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
375 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
376 </output_collection>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
377 <output_collection name="remaining" type="list:paired" count="2">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
378 <element name="reads_R1_0">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
379 <element name="forward">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
380 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
381 <has_size value="20"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
382 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
383 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
384 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
385 <element name="reads_R2_0">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
386 <element name="reverse">
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
387 <assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
388 <has_size value="17607" delta="100"/>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
389 </assert_contents>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
390 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
391 </element>
b4bab607eb05 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents: 2
diff changeset
392 </output_collection>
2
bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
393 </test>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
394 </tests>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
395 <help>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
396 <![CDATA[
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
397 .. class:: infomark
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
398
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
399 **What it does**
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
400
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
401 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but the threshold and window size can be adjusted.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
402
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
403 The process_radtags program can:
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
404
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
405 - handle data that is barcoded, either inline or using an index, or unbarcoded.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
406 - use combinatorial barcodes.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
407 - check and correct for a restriction enzyme cutsite for single or double-digested data.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
408 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
409 - process individual files or whole directories of files.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
410 - directly read gzipped data
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
411 - filter reads based on Illumina's Chastity filter
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
412
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
413 **Help**
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
414
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
415 Input files:
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
416
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
417 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list)
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
418
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
419 - Barcode File
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
420
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
421 The barcode file is a very simple format:
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
422
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
423 ======= ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
424 Barcode Sample name
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
425 ======= ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
426 ATGGGG PopA_01
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
427 GGGTAA PopA_02
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
428 AGGAAA PopA_03
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
429 TTTAAG PopA_04
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
430 GGTGTG PopA_05
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
431 TGATGT PopA_06
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
432 ======= ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
433
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
434 Combinatorial barcodes are specified, one per column, separated by a tab:
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
435
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
436 ======== ======== ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
437 Barcode1 Barcode2 Sample name
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
438 ======== ======== ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
439 CGATA ACGTA PopA_01
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
440 CGGCG CGTA PopA_02
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
441 GAAGC CGTA PopA_03
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
442 GAGAT CGTA PopA_04
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
443 CGATA AGCA PopA_05
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
444 CGGCG AGCA PopA_06
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
445 ======== ======== ===========
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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446
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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447 The sample name column can be omitted. Then the Barcodes are used for naming the output files.
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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448
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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449 @STACKS_INFOS@
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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450 ]]>
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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451 </help>
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bd5ff77e2036 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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452 <expand macro="citation"/>
0
9993234400f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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453 </tool>