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comparison kraken.xml @ 10:766d5f63b0f4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
author iuc
date Tue, 12 Mar 2024 16:10:22 +0000
parents aec58624706f
children
comparison
equal deleted inserted replaced
9:aec58624706f 10:766d5f63b0f4
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 <expand macro="xrefs"/>
9 <expand macro="requirements" /> 10 <expand macro="requirements" />
10 <expand macro="version_command" /> 11 <expand macro="version_command" />
11 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
12 <![CDATA[ 13 <![CDATA[
13 @SET_DATABASE_PATH@ && 14 @SET_DATABASE_PATH@ &&
64 <option value="yes">Paired</option> 65 <option value="yes">Paired</option>
65 <option selected="True" value="no">Single</option> 66 <option selected="True" value="no">Single</option>
66 </param> 67 </param>
67 <when value="collection"> 68 <when value="collection">
68 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> 69 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
69 <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/> 70 <param argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
70 </when> 71 </when>
71 <when value="yes"> 72 <when value="yes">
72 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/> 73 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
73 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/> 74 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
74 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> 75 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
85 help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit"> 86 help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
86 <option value="yes">Yes</option> 87 <option value="yes">Yes</option>
87 <option selected="True" value="no">No</option> 88 <option selected="True" value="no">No</option>
88 </param> 89 </param>
89 <when value="yes"> 90 <when value="yes">
90 <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification" 91 <param argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
91 help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/> 92 help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
92 </when> 93 </when>
93 <when value="no"/><!-- Do absolutely nothing --> 94 <when value="no"/><!-- Do absolutely nothing -->
94 </conditional> 95 </conditional>
95 96
96 <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" 97 <param argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
97 label="Print no Kraken output for unclassified sequences"/> 98 label="Print no Kraken output for unclassified sequences"/>
98 99
99 <expand macro="input_database" /> 100 <expand macro="input_database" />
100 </inputs> 101 </inputs>
101 <outputs> 102 <outputs>
108 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> 109 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
109 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 110 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
110 </outputs> 111 </outputs>
111 112
112 <tests> 113 <tests>
113 <test> 114 <test expect_num_outputs="1">
114 <param name="single_paired_selector" value="no"/> 115 <param name="single_paired_selector" value="no"/>
115 <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/> 116 <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
116 <param name="split_reads" value="false"/> 117 <param name="split_reads" value="false"/>
117 <param name="quick" value="no"/> 118 <param name="quick" value="no"/>
118 <param name="only-classified-output" value="false"/> 119 <param name="only-classified-output" value="false"/>
119 <param name="kraken_database" value="old_style_test_entry"/> 120 <param name="kraken_database" value="old_style_test_entry"/>
120 <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/> 121 <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/>
121 </test> 122 </test>
122 <test> 123 <test expect_num_outputs="1">
123 <param name="single_paired_selector" value="no"/> 124 <param name="single_paired_selector" value="no"/>
124 <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/> 125 <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
125 <param name="split_reads" value="false"/> 126 <param name="split_reads" value="false"/>
126 <param name="quick" value="no"/> 127 <param name="quick" value="no"/>
127 <param name="only-classified-output" value="false"/> 128 <param name="only-classified-output" value="false"/>