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comparison flash.xml @ 7:a46e4079ccd2 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 13:26:25 +0000
parents 147eae9635ec
children
comparison
equal deleted inserted replaced
6:147eae9635ec 7:a46e4079ccd2
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>
4 <xrefs> 3 <xrefs>
5 <xref type="bio.tools">flash</xref> 4 <xref type="bio.tools">flash</xref>
6 </xrefs> 5 </xrefs>
7 <macros> 6 <macros>
98 <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)">
99 <filter>allow_outies and generate_histogram</filter> 98 <filter>allow_outies and generate_histogram</filter>
100 </data> 99 </data>
101 </outputs> 100 </outputs>
102 <tests> 101 <tests>
103 <test> 102 <test expect_num_outputs="5">
104 <param name="select_layout" value="individual" /> 103 <param name="select_layout" value="individual" />
105 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" /> 104 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
106 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" /> 105 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
107 <param name="generate_histogram" value="false" /> 106 <param name="generate_histogram" value="false" />
108 <param name="save_log" value="true" /> 107 <param name="save_log" value="true" />
109 <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" />
110 <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" />
111 <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" />
112 <output name="hist" file="flash_hist_out1.tabular" /> 111 <output name="hist" file="flash_hist_out1.tabular" />
113 <output name="log"> 112 <output name="log">
114 <assert_contents> 113 <assert_contents>
115 <has_line_matching expression=".*Percent combined: 3.60%" /> 114 <has_line_matching expression=".*Percent combined: 3.60%" />
116 </assert_contents> 115 </assert_contents>
117 </output> 116 </output>
118 </test> 117 </test>
119 <test> 118 <test expect_num_outputs="10">
120 <param name="select_layout" value="individual" /> 119 <param name="select_layout" value="individual" />
121 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" /> 120 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
122 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" /> 121 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
123 <param name="allow_outies" value="true" /> 122 <param name="allow_outies" value="true" />
124 <param name="generate_histogram" value="true" /> 123 <param name="generate_histogram" value="true" />
125 <param name="save_log" value="true" /> 124 <param name="save_log" value="true" />
126 <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" />
127 <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" />
128 <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" />
129 <output name="hist" file="flash_hist_out2.tabular" /> 128 <output name="hist" file="flash_hist_out2.tabular" />
130 <output name="histogram" file="flash_hist_out2.txt" /> 129 <output name="histogram" file="flash_hist_out2.txt" />
131 <output name="hist_in" file="flash_hist_in_out2.tabular" /> 130 <output name="hist_in" file="flash_hist_in_out2.tabular" />
132 <output name="histogram_in" file="flash_hist_in_out2.txt" /> 131 <output name="histogram_in" file="flash_hist_in_out2.txt" />
133 <output name="hist_out" file="flash_hist_out_out2.tabular" /> 132 <output name="hist_out" file="flash_hist_out_out2.tabular" />
136 <assert_contents> 135 <assert_contents>
137 <has_line_matching expression=".*Percent combined: 3.80%" /> 136 <has_line_matching expression=".*Percent combined: 3.80%" />
138 </assert_contents> 137 </assert_contents>
139 </output> 138 </output>
140 </test> 139 </test>
141 <test> 140 <test expect_num_outputs="5">
142 <param name="select_layout" value="collection" /> 141 <param name="select_layout" value="collection" />
143 <param name="generate_histogram" value="false" /> 142 <param name="generate_histogram" value="false" />
144 <param name="reads"> 143 <param name="reads">
145 <collection type="paired"> 144 <collection type="paired">
146 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" /> 145 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
147 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" /> 146 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
148 </collection> 147 </collection>
149 </param> 148 </param>
150 <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" />
151 <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" />
152 <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" />
153 <output name="hist" file="flash_hist_out3.tabular" /> 152 <output name="hist" file="flash_hist_out3.tabular" />
154 </test> 153 </test>
155 <test> 154 <test expect_num_outputs="5">
156 <param name="select_layout" value="individual" /> 155 <param name="select_layout" value="individual" />
157 <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" />
158 <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" />
159 <param name="generate_histogram" value="false" /> 158 <param name="generate_histogram" value="false" />
160 <param name="save_log" value="true" /> 159 <param name="save_log" value="true" />
165 <assert_contents> 164 <assert_contents>
166 <has_line_matching expression=".*Percent combined: 3.60%" /> 165 <has_line_matching expression=".*Percent combined: 3.60%" />
167 </assert_contents> 166 </assert_contents>
168 </output> 167 </output>
169 </test> 168 </test>
170 <test> 169 <test expect_num_outputs="5">
171 <param name="select_layout" value="collection" /> 170 <param name="select_layout" value="collection" />
172 <param name="generate_histogram" value="false" /> 171 <param name="generate_histogram" value="false" />
173 <param name="reads"> 172 <param name="reads">
174 <collection type="paired"> 173 <collection type="paired">
175 <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" />