Mercurial > repos > iuc > stacks2_clonefilter

annotate stacks_clonefilter.xml @ 5:42201b90e3f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:26:53 +0000
parents 289b7d6b69a4
children
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42201b90e3f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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10
2
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11 trap ">&2 cat '$output_log'" err exit &&
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12 mkdir stacks_inputs stacks_outputs &&
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13
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14 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
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15 $link_command
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17 clone_filter
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18 #if $input_type.input_type_select == 'single':
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19 -f '$fwd_path'
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20 #else
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21 -1 '$fwd_path'
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22 -2 '$rev_path'
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23 #end if
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25 -i $inputype
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26
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27 -o stacks_outputs
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28 $capture
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29 $input_type.barcode_encoding
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30 #if $oligo_len_1
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31 --oligo_len_1 $oligo_len_1
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32 #end if
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33 #if $oligo_len_2
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34 --oligo_len_2 $oligo_len_2
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35 #end if
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36 $retain_oligo
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37 ## only supports fastq.gz output since the
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38 ## the program outputs empty files for fasta/fastq
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39 -y gzfastq
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40 @TEE_APPEND_LOG@
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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"/>
2
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60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
0
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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"/>
2
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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)"/>
0
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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"/>
3
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68 <expand macro="fastq_output_filter" format="fastqsanger.gz"/>
0
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69 </outputs>
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70 <tests>
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71 <!-- single end, defaults-->
2
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72 <test expect_num_outputs="2">
0
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73 <conditional name="input_type">
2
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74 <param name="input_type_select" value="single"/>
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75 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
0
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76 </conditional>
2
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77 <param name="oligo_len_1" value="6"/>
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78 <param name="add_log" value="yes"/>
3
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79 <assert_command>
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80 <has_text text="--oligo_len_1 6"/>
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81 <not_has_text text="-D"/>
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82 </assert_command>
1
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83 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
3
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84 <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
0
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85 </test>
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86 <!-- single end, alt BCencoding, capture-->
2
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87 <test expect_num_outputs="3">
0
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88 <conditional name="input_type">
2
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89 <param name="input_type_select" value="single"/>
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90 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
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91 <param name="barcode_encoding" value="--index_null"/>
0
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92 </conditional>
3
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93 <param name="capture" value="true"/>
2
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94 <param name="oligo_len_1" value="6"/>
0
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95 <assert_command>
3
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96 <has_text text="--oligo_len_1 6"/>
2
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97 <has_text text="-D"/>
0
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98 </assert_command>
2
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99 <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
3
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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100 <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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101 <output name="discarded" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
0
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102 </test>
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103 <!-- paired end, defaults-->
2
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104 <test expect_num_outputs="4">
0
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105 <conditional name="input_type">
2
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106 <param name="input_type_select" value="paired"/>
0
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107 <param name="fqinputs">
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108 <collection type="paired">
2
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109 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
2f1d464ebfd2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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110 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
0
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111 </collection>
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112 </param>
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113 </conditional>
2
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114 <param name="oligo_len_1" value="6"/>
3
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115 <assert_command>
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116 <has_text text="--oligo_len_1 6"/>
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117 <not_has_text text="--oligo_len_2"/>
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118 <not_has_text text="-D"/>
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119 </assert_command>
2
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120 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
3
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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121 <output_collection name="clean_pair" type="paired" count="2"/>
0
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122 </test>
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123 <!-- paired end, non defaults -->
2
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124 <test expect_num_outputs="7">
0
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125 <conditional name="input_type">
2
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126 <param name="input_type_select" value="paired"/>
0
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127 <param name="fqinputs">
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128 <collection type="paired">
2
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129 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
2f1d464ebfd2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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130 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
0
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131 </collection>
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132 </param>
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133 </conditional>
2
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134 <param name="oligo_len_1" value="6"/>
3
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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135 <param name="oligo_len_2" value="6"/>
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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136 <param name="capture" value="true"/>
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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137 <param name="retain_oligo" value="true"/>
0
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138 <assert_command>
3
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139 <has_text text="--oligo_len_1 6"/>
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140 <has_text text="--oligo_len_2 6"/>
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141 <has_text text="-D"/>
2
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142 <has_text text="--retain_oligo"/>
0
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143 </assert_command>
2
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144 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
3
289b7d6b69a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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145 <output_collection name="clean_pair" type="paired" count="2"/>
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146 <output_collection name="discarded_pair" type="paired" count="2"/>
0
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147 </test>
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148 </tests>
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149 <help>
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150 <![CDATA[
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151 .. class:: infomark
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152
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153 The clone_filter program is designed to identify PCR clones.
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154
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155 @STACKS_INFOS@
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156 ]]>
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157 </help>
2
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158 <expand macro="citation"/>
0
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159 </tool>