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comparison cmstat.xml @ 5:6e18e0b098cd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author bgruening
date Sat, 21 Jan 2017 17:36:57 -0500
parents 2c2c5e5e495b
children c9e29ac5d099
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4:c47a7c52ac4f 5:6e18e0b098cd
1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1"> 1 <tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
2 <description>for covariance model (cmstat)</description> 2 <description>Summary statistics for covariance model </description>
3 <requirements> 3 <macros>
4 <requirement type="package">infernal</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.1">infernal</requirement> 5 </macros>
6 <requirement type="package" version="8.22">gnu_coreutils</requirement> 6 <expand macro="requirements"/>
7 </requirements> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy 10 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
11 ## it will be converted to a tab delimited file and piped to Galaxy 11 ## it will be converted to a tab delimited file and piped to Galaxy
12 temp_tabular_output=\$(mktemp); 12 ##temp_tabular_output=\$(mktemp);
13 13
14 cmstat 14 cmstat
15
16 #if str($cm_opts.cm_opts_selector) == "db": 15 #if str($cm_opts.cm_opts_selector) == "db":
17 $cm_opts.database.fields.path 16 $cm_opts.database.fields.path
18 #else: 17 #else:
19 $cm_opts.cmfile 18 $cm_opts.cmfile
20 #end if 19 #end if
21 20
22 > \$temp_tabular_output 21 > $outfile
23 ;
24 22
25 ## 1. replace all lines starting # (comment lines)
26 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
27 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
28 23
29 ]]> 24 ]]>
30 </command> 25 </command>
31 <inputs> 26 <inputs>
32 <conditional name="cm_opts"> 27 <conditional name="cm_opts">
49 </conditional> 44 </conditional>
50 </inputs> 45 </inputs>
51 <outputs> 46 <outputs>
52 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/> 47 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
53 </outputs> 48 </outputs>
49 <tests>
50 <test>
51 <conditional name="cm_opts">
52 <param name="cm_opts_selector" value="histdb"/>
53 <param name="cmfile" value="cmstat_input.cm"/>
54 </conditional>
55 <output name="outfile" >
56 <assert_contents>
57 <has_text text="idx"/>
58 <has_text text="accession"/>
59 <has_text text="nseq"/>
60 </assert_contents>
61 </output>
62 </test>
63 </tests>
54 <help> 64 <help>
55 <![CDATA[ 65 <![CDATA[
56 66
57 67
58 **What it does** 68 **What it does**
84 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”. 94 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
85 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM 95 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
86 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs. 96 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
87 97
88 98
89 For further questions please refere to the Infernal `Userguide <http://selab.janelia.org/software/infernal/Userguide.pdf>`_. 99 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
90 100
91 ]]> 101 ]]>
92 </help> 102 </help>
93 <citations> 103 <expand macro="citations" />
94 <citation type="doi">10.1093/bioinformatics/btt509</citation> 104
95 <citation type="bibtex">
96 @ARTICLE{bgruening_galaxytools,
97 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
98 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
99 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
100 url = {https://github.com/bgruening/galaxytools}
101 }
102 </citation>
103 </citations>
104
105
106 </tool> 105 </tool>