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comparison cmstat.xml @ 2:fac157e22e1b draft

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author bgruening
date Fri, 13 Feb 2015 03:10:51 -0500
parents 652f9d550531
children 2c2c5e5e495b
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1:55bb96edfc07 2:fac157e22e1b
1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1"> 1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
2 <description>for covariance model (cmstat)</description> 2 <description>for covariance model (cmstat)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">infernal</requirement> 4 <requirement type="package">infernal</requirement>
5 <requirement type="package" version="1.1">infernal</requirement> 5 <requirement type="package" version="1.1">infernal</requirement>
6 <requirement type="package" version="8.21">gnu_coreutils</requirement> 6 <requirement type="package" version="8.22">gnu_coreutils</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[
9 ## 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
10 ## 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
11 temp_tabular_output=\$(mktemp); 12 temp_tabular_output=\$(mktemp);
12 13
13 cmstat 14 cmstat
23 24
24 ## 1. replace all lines starting # (comment lines) 25 ## 1. replace all lines starting # (comment lines)
25 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces) 26 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
26 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile 27 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
27 28
29 ]]>
28 </command> 30 </command>
29 <inputs> 31 <inputs>
30 <conditional name="cm_opts"> 32 <conditional name="cm_opts">
31 <param name="cm_opts_selector" type="select" label="Subject covariance models"> 33 <param name="cm_opts_selector" type="select" label="Subject covariance models">
32 <option value="db" selected="True">Locally installed covariance models</option> 34 <option value="db" selected="True">Locally installed covariance models</option>
48 </inputs> 50 </inputs>
49 <outputs> 51 <outputs>
50 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/> 52 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
51 </outputs> 53 </outputs>
52 <help> 54 <help>
55 <![CDATA[
53 56
54 57
55 **What it does** 58 **What it does**
56 59
57 The cmstat utility prints out a tabular file of summary statistics for each given covariance model. 60 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
59 62
60 Output format 63 Output format
61 ------------- 64 -------------
62 65
63 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a 66 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
64 tabular format. 67 tabular format.
65 68
66 The columns are: 69 The columns are:
67 70
68 (1) The index of this profile, numbering each on in the file starting from 1. 71 (1) The index of this profile, numbering each on in the file starting from 1.
69 (2) The name of the profile. 72 (2) The name of the profile.
89 92
90 93
91 How do I cite Infernal? 94 How do I cite Infernal?
92 ----------------------- 95 -----------------------
93 96
94 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013). 97 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
95 98
96 **Galaxy Wrapper Author**:: 99 **Galaxy Wrapper Author**::
97 100
98 * Bjoern Gruening, University of Freiburg 101 * Bjoern Gruening, University of Freiburg
99 102
103 ]]>
100 </help> 104 </help>
101 </tool> 105 </tool>