Mercurial > repos > bgruening > infernal

comparison cmstat.xml @ 9:1d74ed49cf41 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
comparison
equal deleted inserted replaced
8:c9e29ac5d099 9:1d74ed49cf41
1 <tool id="infernal_cmstat" name="cmstat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="infernal_cmstat" name="cmstat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Summary statistics for covariance model </description> 2 <description>Summary statistics for covariance model </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio" /> 8 <expand macro="stdio" />
8 <expand macro="xrefs"/>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy 11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
12 ## it will be converted to a tab delimited file and piped to Galaxy 12 ## it will be converted to a tab delimited file and piped to Galaxy
13 ##temp_tabular_output=\$(mktemp); 13 ##temp_tabular_output=\$(mktemp);
23 23
24 24
25 ]]> 25 ]]>
26 </command> 26 </command>
27 <inputs> 27 <inputs>
28 <conditional name="cm_opts"> 28 <expand macro="DB" />
29 <param name="cm_opts_selector" type="select" label="Subject covariance models">
30 <option value="db" selected="True">Locally installed covariance models</option>
31 <option value="histdb">Covariance model from your history</option>
32 </param>
33 <when value="db">
34 <param name="database" type="select" label="Covariance models">
35 <options from_file="infernal.loc">
36 <column name="value" index="0"/>
37 <column name="name" index="1"/>
38 <column name="path" index="2"/>
39 </options>
40 </param>
41 </when>
42 <when value="histdb">
43 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
44 </when>
45 </conditional>
46 </inputs> 29 </inputs>
47 <outputs> 30 <outputs>
48 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/> 31 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
49 </outputs> 32 </outputs>
50 <tests> 33 <tests>
51 <test> 34 <test>
52 <conditional name="cm_opts"> 35 <conditional name="cm_opts">
53 <param name="cm_opts_selector" value="histdb"/> 36 <param name="cm_opts_selector" value="histdb"/>
54 <param name="cmfile" value="cmstat_input.cm"/> 37 <param name="cmfile" value="cmstat_input.cm"/>
38 </conditional>
39 <output name="outfile" >
40 <assert_contents>
41 <has_text text="idx"/>
42 <has_text text="accession"/>
43 <has_text text="nseq"/>
44 </assert_contents>
45 </output>
46 </test>
47 <test>
48 <conditional name="cm_opts">
49 <param name="cm_opts_selector" value="db"/>
50 <param name="database" value="cmstat_input.cm"/>
55 </conditional> 51 </conditional>
56 <output name="outfile" > 52 <output name="outfile" >
57 <assert_contents> 53 <assert_contents>
58 <has_text text="idx"/> 54 <has_text text="idx"/>
59 <has_text text="accession"/> 55 <has_text text="accession"/>