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comparison kraken2.xml @ 5:20e2f64aa1fe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit b5beeef6c90fe39ce3ace531877d632725839ee4
author iuc
date Fri, 09 Feb 2024 21:43:22 +0000
parents e674066930b2
children
comparison
equal deleted inserted replaced
4:e674066930b2 5:20e2f64aa1fe
4 assign taxonomic labels to sequencing reads 4 assign taxonomic labels to sequencing reads
5 </description> 5 </description>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <xrefs>
10 <xref type="bio.tools">kraken2</xref>
11 </xrefs>
9 <requirements> 12 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
11 </requirements> 14 </requirements>
12 <version_command>kraken2 --version</version_command> 15 <version_command>kraken2 --version</version_command>
13 <command detect_errors="exit_code"> 16 <command detect_errors="exit_code">
113 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>
114 </data> 117 </data>
115 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads"> 118 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 119 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>
117 </data> 120 </data>
118 <data name="report_output" format="tabular" label="Report: ${tool.name} on ${on_string}"> 121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
119 <filter>(report['create_report'])</filter> 122 <filter>(report['create_report'])</filter>
120 </data> 123 </data>
121 124
122 <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*"> 125 <data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*">
123 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> 126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
124 </data> 127 </data>
125 <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*"> 128 <data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*">
126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> 129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
127 </data> 130 </data>
128 <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*"> 131 <data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*">
129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> 132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
130 </data> 133 </data>
131 <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*"> 134 <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*">
132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> 135 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
133 </data> 136 </data>
134 137
135 <data name="out1_1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*"> 138 <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*">
136 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
137 </data> 140 </data>
138 <data name="out2_1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*"> 141 <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*">
139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
140 </data> 143 </data>
141 <data name="out3_1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*"> 144 <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*">
142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
143 </data> 146 </data>
144 <data name="out4_1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*"> 147 <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*">
145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 148 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
146 </data> 149 </data>
147 150
148 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> 151 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
149 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 152 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
150 </outputs> 153 </outputs>
151 <tests> 154 <tests>
152 <test> 155 <test expect_num_outputs="1">
153 <param name="single_paired_selector" value="no"/> 156 <param name="single_paired_selector" value="no"/>
154 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> 157 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
155 <param name="split_reads" value="false"/> 158 <param name="split_reads" value="false"/>
156 <param name="quick" value="no"/> 159 <param name="quick" value="no"/>
157 <param name="confidence" value=".2"/> 160 <param name="confidence" value=".2"/>
158 <param name="kraken2_database" value="test_entry"/> 161 <param name="kraken2_database" value="test_entry"/>
159 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> 162 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
160 </test> 163 </test>
161 <test> 164 <test expect_num_outputs="5">
162 <param name="single_paired_selector" value="yes"/> 165 <param name="single_paired_selector" value="yes"/>
163 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> 166 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
164 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> 167 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
165 <param name="split_reads" value="true"/> 168 <param name="split_reads" value="true"/>
166 <param name="quick" value="no"/> 169 <param name="quick" value="no"/>
169 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> 172 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
170 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> 173 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
171 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> 174 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
172 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/> 175 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
173 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> 176 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
174
175 </test> 177 </test>
176 <test> 178 <test expect_num_outputs="2">
177 <param name="single_paired_selector" value="yes"/> 179 <param name="single_paired_selector" value="yes"/>
178 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> 180 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
179 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> 181 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
180 <param name="use-names" value="true"/> 182 <param name="use-names" value="true"/>
181 <section name="report"> 183 <section name="report">