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comparison flash.xml @ 6:01a4ebf1f237 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 7e92326c8481e440066c4aabb13d373dec570e2e
author iuc
date Wed, 06 Jul 2022 13:27:05 +0000
parents a27654fc4270
children
comparison
equal deleted inserted replaced
5:a27654fc4270 6:01a4ebf1f237
1 <?xml version="1.0"?> 1 <tool id="flash" name="FLASH" version="@VERSION@.4" profile="21.05">
2 <tool id="flash" name="FLASH" version="@VERSION@.4">
3 <description>adjust length of short reads</description> 2 <description>adjust length of short reads</description>
3 <xrefs>
4 <xref type="bio.tools">flash</xref>
5 </xrefs>
4 <macros> 6 <macros>
5 <token name="@VERSION@">1.2.11</token> 7 <token name="@VERSION@">1.2.11</token>
6 </macros> 8 </macros>
7 <requirements> 9 <requirements>
8 <requirement type="package" version="@VERSION@">flash</requirement> 10 <requirement type="package" version="@VERSION@">flash</requirement>
95 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)"> 97 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
96 <filter>allow_outies and generate_histogram</filter> 98 <filter>allow_outies and generate_histogram</filter>
97 </data> 99 </data>
98 </outputs> 100 </outputs>
99 <tests> 101 <tests>
100 <test> 102 <test expect_num_outputs="5">
101 <param name="select_layout" value="individual" /> 103 <param name="select_layout" value="individual" />
102 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" /> 104 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
103 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" /> 105 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
104 <param name="generate_histogram" value="false" /> 106 <param name="generate_histogram" value="false" />
105 <param name="save_log" value="true" /> 107 <param name="save_log" value="true" />
106 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" /> 108 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" sort="true" />
107 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" /> 109 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" sort="true" />
108 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" /> 110 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" sort="true" />
109 <output name="hist" file="flash_hist_out1.tabular" /> 111 <output name="hist" file="flash_hist_out1.tabular" />
110 <output name="log"> 112 <output name="log">
111 <assert_contents> 113 <assert_contents>
112 <has_line_matching expression=".*Percent combined: 3.60%" /> 114 <has_line_matching expression=".*Percent combined: 3.60%" />
113 </assert_contents> 115 </assert_contents>
114 </output> 116 </output>
115 </test> 117 </test>
116 <test> 118 <test expect_num_outputs="10">
117 <param name="select_layout" value="individual" /> 119 <param name="select_layout" value="individual" />
118 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" /> 120 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
119 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" /> 121 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
120 <param name="allow_outies" value="true" /> 122 <param name="allow_outies" value="true" />
121 <param name="generate_histogram" value="true" /> 123 <param name="generate_histogram" value="true" />
122 <param name="save_log" value="true" /> 124 <param name="save_log" value="true" />
123 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" /> 125 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" sort="true" />
124 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" /> 126 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" sort="true" />
125 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" /> 127 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" sort="true" />
126 <output name="hist" file="flash_hist_out2.tabular" /> 128 <output name="hist" file="flash_hist_out2.tabular" />
127 <output name="histogram" file="flash_hist_out2.txt" /> 129 <output name="histogram" file="flash_hist_out2.txt" />
128 <output name="hist_in" file="flash_hist_in_out2.tabular" /> 130 <output name="hist_in" file="flash_hist_in_out2.tabular" />
129 <output name="histogram_in" file="flash_hist_in_out2.txt" /> 131 <output name="histogram_in" file="flash_hist_in_out2.txt" />
130 <output name="hist_out" file="flash_hist_out_out2.tabular" /> 132 <output name="hist_out" file="flash_hist_out_out2.tabular" />
133 <assert_contents> 135 <assert_contents>
134 <has_line_matching expression=".*Percent combined: 3.80%" /> 136 <has_line_matching expression=".*Percent combined: 3.80%" />
135 </assert_contents> 137 </assert_contents>
136 </output> 138 </output>
137 </test> 139 </test>
138 <test> 140 <test expect_num_outputs="5">
139 <param name="select_layout" value="collection" /> 141 <param name="select_layout" value="collection" />
140 <param name="generate_histogram" value="false" /> 142 <param name="generate_histogram" value="false" />
141 <param name="reads"> 143 <param name="reads">
142 <collection type="paired"> 144 <collection type="paired">
143 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" /> 145 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
144 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" /> 146 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
145 </collection> 147 </collection>
146 </param> 148 </param>
147 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" /> 149 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" sort="true" />
148 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" /> 150 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" sort="true" />
149 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" /> 151 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" sort="true" />
150 <output name="hist" file="flash_hist_out3.tabular" /> 152 <output name="hist" file="flash_hist_out3.tabular" />
151 </test> 153 </test>
152 <test> 154 <test expect_num_outputs="5">
153 <param name="select_layout" value="individual" /> 155 <param name="select_layout" value="individual" />
154 <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> 156 <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
155 <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> 157 <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
156 <param name="generate_histogram" value="false" /> 158 <param name="generate_histogram" value="false" />
157 <param name="save_log" value="true" /> 159 <param name="save_log" value="true" />
162 <assert_contents> 164 <assert_contents>
163 <has_line_matching expression=".*Percent combined: 3.60%" /> 165 <has_line_matching expression=".*Percent combined: 3.60%" />
164 </assert_contents> 166 </assert_contents>
165 </output> 167 </output>
166 </test> 168 </test>
167 <test> 169 <test expect_num_outputs="5">
168 <param name="select_layout" value="collection" /> 170 <param name="select_layout" value="collection" />
169 <param name="generate_histogram" value="false" /> 171 <param name="generate_histogram" value="false" />
170 <param name="reads"> 172 <param name="reads">
171 <collection type="paired"> 173 <collection type="paired">
172 <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" /> 174 <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" />