diff sequence2gspan.xml @ 0:b01beb170290 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequence2gspan.xml	Tue Oct 29 11:10:19 2013 -0400
@@ -0,0 +1,167 @@
+<tool id="sequence2gpsan_rnashapes" name="Sequence to gspan" version="0.3">
+    <description>converter using RNAshapes</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.1.6">rnashapes</requirement>
+    </requirements>
+    <command interpreter="perl">
+
+        fasta2shrep_gspan.pl
+            --fasta $infile
+
+            #if $annotate_infile:
+                -annotate $annotate_infile
+            #end if
+
+            -shift $shift
+            $cue
+            $stack
+            #if $energy_opts.energy_opts_selector == 'energy':
+                -e $energy_opts.e
+            #elif $energy_opts.energy_opts_selector == 'rel_energy':
+                -c $energy_opts.c
+            #end if
+
+            #if $structure_sampling_opts.structure_sampling_opts_selector == 'on':
+                -i $structure_sampling_opts.i
+                -sample_len $structure_sampling_opts.sample_len
+            #end if
+
+            $q
+            -Tp $Tp
+            $seq_graph_win
+            $seq_graph_t
+            $seq_graph_alph
+            $abstr
+            $nostr
+            $vp
+            $ignore_header
+            -M $M
+            $u
+            $r
+
+            -stdout
+
+            > $output
+
+    </command>
+    <inputs>
+        <param name="ifile" type="data" format="fasta" label="Nucleotide Sequence in FASTA format"/>
+
+        <!-- todo repeat tag, normally only 3 windows are specified-->
+        <param name="wins" type="text" value="" label="A list of window sizes to use"
+            help="if none are given, then the entire sequence is taken with no windows. Each window > 1 required! Example: 50,100,200. (-wins)" />
+        <param name="t" type="text" value="3=0" label="The shape type (RNAshapes types from 1-5)"
+            help="With the list format, the shape level can be changed for different window length '4=100' means that shape level 4 is used from length 100nt (window length) The first given length has to be 0! Not continuous given levels are allowed! (-t)" />
+
+
+        <param name="shift" type="integer" value="1" label="The shift of the window, relative to the window size given in percent" 
+            help="Example 20 % of a window 150 would result in a step size of 30 nt. It is a relative parameter, as you can give different window sizes. Default shift of 1 nt. (-shift)">
+            <validator type="in_range" min="0" max="100" />
+        </param>
+        <param name="cue" type="boolean" label="Crop unpaired ends" truevalue="-cue" falsevalue="" checked="false" 
+            help="If you give this flag, then the unpaired ends of each single structure are ignored. E.g. the structure ...(((...))).. becomes just (((...))). (-cue)" />
+
+        <param name="stack" type="boolean" label="Adds stacking information to graphs" truevalue="-stack" falsevalue="" checked="false" 
+            help="This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges (type p) from each of the involved bases to the new vertex. (-stack)" />
+
+        <conditional name="energy_opts">
+            <param name="energy_opts_selector" type="select" label="Energy calculation mode">
+                <option value="rel_energy">Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)</option>
+                <option value="energy">Energy range in kcal/mol (RNAshapes)</option>
+                <option value="">None</option>
+            </param>
+            <when value="" />
+            <when value="energy">
+                <param name="e" type="float" value="5.0" label="Energy range in kcal/mol (RNAshapes)" help="-e">
+                    <validator type="in_range" min="0.0" />
+                </param>
+            </when>
+            <when value="rel_energy">
+                <param name="c" type="float" value="10" label="Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="(-c)">
+                    <validator type="in_range" min="0.0" />
+                </param>
+            </when>
+        </conditional>
+        <param name="M" type="integer" value="0" label="Max number of shreps that should be taken per window" help="0 means selects all shreps. (-M)">
+            <validator type="in_range" min="0" />
+        </param>
+        <param name="u" type="boolean" label="Ignore unstable RNAshapes" truevalue="-u" falsevalue="" checked="false" 
+            help="This option filters out closed structures with positive free energy. (-u)" />
+
+        <param name="r" type="boolean" label="Calculate structure probabilities for RNAshapes" help="(-r)" truevalue="-r" falsevalue="" checked="false" />
+
+
+        <conditional name="structure_sampling_opts">
+            <param name="structure_sampling_opts_selector" type="select" label="Structure Sampling">
+                <option value="on">On</option>
+                <option value="off">Off</option>
+            </param>
+            <when value="on">
+                <param name="i" type="integer" value="1" label="Number of sampling iterations" help="(-i)">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="smaple_len" type="integer" value="0" label="Sampling is only used for seqs/windows >= given length" help="Default 0 (sample all length). (-sample-len)">
+                    <validator type="in_range" min="0" />
+                </param>
+            </when>
+            <when value="off" />
+        </conditional>
+
+        <param name="q" type="boolean" label="Turn on shape probabilities for RNAshapes, no sampling mode allowed" help="(-q)" truevalue="-q" falsevalue="" checked="false" />
+        <param name="Tp" type="float" value="0.001" label="Filter cutoff for shape probabilities, applied before -M filter!" help="(-Tp)">
+            <validator type="in_range" min="0.0" />
+        </param>
+
+        <param name="seq_graph_win" type="boolean" label="Add for each window a graph which contains no structure" 
+            help="(-seq-graph-win)" 
+            truevalue="-seq-graph-win" falsevalue="" checked="false" />
+        <param name="seq_graph_t" type="boolean" label="add for each 't #' a graph which contains no structure" 
+            help="(-seq-graph-t)" 
+            truevalue="-seq-graph-t" falsevalue="" checked="false" />
+        <param name="seq_graph_alph" type="boolean" label="Change the alphabet of unstructured graphs" 
+            help="(-seq-graph-alph)" 
+            truevalue="-seq-graph-alph" falsevalue="" checked="false" />
+
+        <param format="tabular" name="annotate_infile" type="data" optional="True" label="A file with annotations to be added as abstract graphs" 
+            help="The format is has the following TAB-delimited columns: SEQID, START, END, NAMESPACE#LABEL. Labels with the same name-space and SEQID form connected components, which is a sequence of label vertices ordered by the START position in the sequence."/>
+
+        <param name="abstr" type="boolean" label="Add abstract structure graphs to the single shrep graph instances" 
+            help="(-abstr)" 
+            truevalue="-abstr" falsevalue="" checked="false" />
+        <param name="nostr" type="boolean" label="Calculate no structures, only add sequence information" 
+            help="-seq-graph-win AND/OR -seq-graph-t are required (-nostr)" 
+            truevalue="-nostr" falsevalue="" checked="false" />
+
+        <!--
+            -match-shape    SHAPE
+            all seqs/windows will be constraint folded into that shape via 
+            RNAshapes (if structure is given in another way this struct will be kept), 
+            if this shape is not possible within given energy range, produce a 
+            specific t graph with only one vertex 'X'. By this the instance 
+            becomes very unsimilar to all other graphs (for knn)
+        -->
+        <param name="vp" type="boolean" label="Enable graph computation with viewpoints" 
+            help="svmsgdnspdk will center on those nucleotides that are given via capital letters and ignore those given as lowercase letters (-vp)" 
+            truevalue="-vp" falsevalue="" checked="false" />
+
+        <param name="ignore_header" type="boolean" label="Don't write fasta id part after first space to gspan" help="(-ignore-header)" truevalue="-ignore-header" falsevalue="" checked="false" />
+
+    </inputs>
+    <outputs>
+        <data format="gspan" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+**What it does**
+
+
+
+**References**
+
+Sita et al...
+
+    </help>
+</tool>