Mercurial > repos > bgruening > infernal

comparison cmpress.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_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description> Prepare a covariance model database for cmscan</description> 2 <description> Prepare a covariance model database for cmscan</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 detect_errors="aggressive">
9 <command>
10 <![CDATA[ 10 <![CDATA[
11 ## CM file from the history or stored as database on disc 11 mkdir -p ./cm_model &&
12 #if str($cm_opts.cm_opts_selector) == "db": 12 #if str($cm_opts.cm_opts_selector) == "db":
13 cmfile_path='$cm_opts.database.fields.path' 13 ln -s '$cm_opts.database.fields.path' ./cm_model/
14 #else: 14 #else:
15 ##'$cm_opts.cmfile' 15 ln -s '$cmfile' ./cm_model/
16 cmfile_path='$cmfile'
17 #end if 16 #end if
18 && 17 &&
19 cmpress -F "\$cmfile_path" && 18 cmpress -F ./cm_model/* &&
20 ##cmpress creates four files in the same directory of the cm file 19 cd ./cm_model/ &&
21 cd `dirname "\$cmfile_path"` && 20 tar -cvf '$outfile' *.i1f *.i1i *.i1m *.i1p
22 tar -cvf '$outfile' `basename "\$cmfile_path"`.i1*
23 ]]> 21 ]]>
24 </command> 22 </command>
25 <inputs> 23 <inputs>
26 <conditional name="cm_opts"> 24 <expand macro="DB" />
27 <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
28 <option value="db" >Locally installed covariance models</option>
29 <option value="histdb" selected="True">Covariance model from your history</option>
30 </param>
31 <when value="db">
32 <param name="database" type="select" label="Covariance models">
33 <options from_file="infernal.loc">
34 <column name="value" index="0"/>
35 <column name="name" index="1"/>
36 <column name="path" index="2"/>
37 </options>
38 </param>
39 </when>
40 <when value="histdb">
41 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
42 </when>
43 </conditional>
44
45 </inputs> 25 </inputs>
46 <outputs> 26 <outputs>
47 <data format="tar" name="outfile" label="cmpress on ${on_string}"/> 27 <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
48 </outputs> 28 </outputs>
49 29
56 <assert_stdout> 36 <assert_stdout>
57 <has_text text="Working... done."/> 37 <has_text text="Working... done."/>
58 </assert_stdout> 38 </assert_stdout>
59 39
60 </test> 40 </test>
41 <test>
42 <conditional name="cm_opts">
43 <param name="cm_opts_selector" value="db"/>
44 <param name="database" value="cmpress_input_minifam.cm"/>
45 </conditional>
46 <assert_stdout>
47 <has_text text="Working... done."/>
48 </assert_stdout>
61 49
50 </test>
62 </tests> 51 </tests>
63 <help> 52 <help>
64 <![CDATA[ 53 <![CDATA[
65 54
66 55