diff cmstat.xml @ 9:1aa4c036e41c draft

Uploaded

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+++ b/cmstat.xml	Sat Sep 07 16:14:02 2013 -0400
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+<tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.0">
+    <description>for covariance model (cmstat)</description>
+    <requirements>
+        <requirement type="package">infernal</requirement>
+        <requirement type="package" version="1.1rc4">infernal</requirement>
+        <requirement type="package" version="8.21">gnu_coreutils</requirement>
+    </requirements>
+    <command>
+        ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
+        ## it will be converted to a tab delimited file and piped to Galaxy
+        temp_tabular_output=\$(mktemp);
+
+        cmstat
+
+            #if $cm_opts.cm_opts_selector == "db":
+                $cm_opts.database.fields.path
+            #else:
+                $cm_opts.cmfile
+            #end if
+
+            > \$temp_tabular_output
+            ;
+
+            ## 1. replace all lines starting # (comment lines)
+            ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
+            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
+
+    </command>
+        <inputs>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" type="select" label="Subject covariance models">
+                  <option value="db" selected="True">Locally installed covariance models</option>
+                  <option value="histdb">Covariance model from your history</option>
+                </param>
+                <when value="db">
+                    <param name="database" type="select" label="Covariance models">
+                        <options from_file="infernal.loc">
+                          <column name="value" index="0"/>
+                          <column name="name" index="1"/>
+                          <column name="path" index="2"/>
+                        </options>
+                    </param>
+                </when>
+                <when value="histdb">
+                    <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
+                </when>
+            </conditional>
+        </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>
+    </outputs>
+    <help>
+
+
+**What it does**
+
+The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
+
+
+Output format
+-------------
+
+By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
+tabular format. 
+
+The columns are:
+
+(1) The index of this profile, numbering each on in the file starting from 1.
+(2) The name of the profile.
+(3) The optional accession of the profile, or ”-” if there is none.
+(4) The number of sequences that the profile was estimated from.
+(5) The effective number of sequences that the profile was estimated from, after Infernal applied an effective sequence number calculation such as the default entropy weighting.
+(6) The length of the model in consensus residues (match states).
+(7) The expected maximum length of a hit to the model.
+(8) The number of basepairs in the model.
+(9) The number of bifurcations in the model.
+(10) What type of model will be used by default in cmsearch and cmscan for this profile, either ”cm” or ”hmm”. For profiles with 0 basepairs, this will be ”hmm” (unless the --nohmmonly option is used). For all other profiles, this will be ”cm”.
+(11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
+     sensus position. This is what the default entropy-weighting method for effective sequence
+     number estimation focuses on, so for default Infernal, this value will often reflect the default
+     target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
+(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
+     relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
+
+
+For further questions please refere to the Infernal Userguide_.
+
+.. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
+
+
+How do I cite Infernal?
+-----------------------
+
+The Infernal 1.0 paper (Nawrocki et al., 2009) is the best paper to reference. 
+If you’re writing for an enlightened (url-friendly) journal, you may want to cite the webpage
+http://infernal.janelia.org/ because it is kept up-to-date. We hope to publish a paper related to
+Infernal version 1.1 soon.
+
+**Galaxy Wrapper Author**::
+
+    *  Bjoern Gruening, University of Freiburg
+
+    </help>
+</tool>