Mercurial > repos > iuc > obi_annotate

comparison obiannotate.xml @ 3:b93ce09eb109 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:32:31 +0000
parents 84c2bf47c50f
children d0f6ac976373
comparison
equal deleted inserted replaced
2:773373a4dafa 3:b93ce09eb109
1 <tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@"> 1 <tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Adds/Edits sequence record annotations</description> 2 <description>Adds/Edits sequence record annotations</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command> 8 <command><![CDATA[
9 @GUNZIP_INPUT@
9 10
10 <![CDATA[
11 obiannotate 11 obiannotate
12 --without-progress-bar
12 ${seqrank} 13 ${seqrank}
13 14
14 #if $rename_tag.old_name and $rename_tag.new_name 15 #if $rename_tag.old_name and $rename_tag.new_name
15 -R '$rename_tag.old_name':'$rename_tag.new_name' 16 -R '$rename_tag.old_name':'$rename_tag.new_name'
16 #end if 17 #end if
68 #end if 69 #end if
69 70
70 #if $mclfile 71 #if $mclfile
71 --mcl='$mclfile' 72 --mcl='$mclfile'
72 #end if 73 #end if
73 74 @INPUT_FORMAT@
74 '$inputseq' > '$output' 75 @OUT_FORMAT@
75 ]]> 76 input
76 77 @GZIP_OUTPUT@
77 </command> 78 > '$output'
79
80 @GENERATE_GALAXY_JSON@
81 ]]></command>
78 82
79 <inputs> 83 <inputs>
80 <param name="inputseq" type="data" format="fastq,fasta" label="Input sequences file" /> 84 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
81 <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" /> 85 <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" />
82 <section name="rename_tag" title="Rename attribute" expanded="False"> 86 <section name="rename_tag" title="Rename attribute" expanded="False">
83 <param name="old_name" type="text" label="old name" optional="true"/> 87 <param name="old_name" type="text" label="old name" optional="true"/>
84 <param name="new_name" type="text" label="new name" optional="true"/> 88 <param name="new_name" type="text" label="new name" optional="true"/>
85 </section> 89 </section>
115 <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/> 119 <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/>
116 120
117 <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" /> 121 <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" />
118 122
119 <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" /> 123 <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" />
120 124 <expand macro="input_format_options_macro"/>
125 <expand macro="out_format_macro"/>
121 </inputs> 126 </inputs>
122 <outputs> 127 <outputs>
123 <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" /> 128 <data name="output" format="auto"/>
124 </outputs> 129 </outputs>
125
126 <tests> 130 <tests>
127 <test> 131 <test>
128 <param name="inputseq" value="output_obiuniq.fasta" /> 132 <param name="input" value="output_obiuniq.fasta" ftype="fasta"/>
129 <section name="key_selector"> 133 <section name="key_selector">
130 <param name="key" value="count" /> 134 <param name="key" value="count" />
131 <param name="key2" value="merged_sample" /> 135 <param name="key2" value="merged_sample" />
132 </section> 136 </section>
133 <param name="uniqid" value="true" /> 137 <param name="uniqid" value="true" />
135 <param name="length" value="true" /> 139 <param name="length" value="true" />
136 <param name="seqrank" value="true" /> 140 <param name="seqrank" value="true" />
137 141
138 <output name="output" file="output_obiannotate.fasta" ftype="fasta"/> 142 <output name="output" file="output_obiannotate.fasta" ftype="fasta"/>
139 </test> 143 </test>
144 <test>
145 <param name="input" value="output_obiuniq.fasta.gz" ftype="fasta.gz"/>
146 <section name="key_selector">
147 <param name="key" value="count" />
148 <param name="key2" value="merged_sample" />
149 </section>
150 <param name="uniqid" value="true" />
151 <param name="clearbool" value="true" />
152 <param name="length" value="true" />
153 <param name="seqrank" value="true" />
154 <output name="output" file="output_obiannotate.fasta.gz" ftype="fasta.gz" decompress="true"/>
155 </test>
156 <!-- TODO fastq input test -->
140 </tests> 157 </tests>
141 158
142 <help><![CDATA[ 159 <help><![CDATA[
143 160
144 .. class:: infomark 161 .. class:: infomark