diff lastsplit.xml @ 0:9a7e91fc6562 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastsplit.xml	Wed Jun 17 14:50:21 2020 -0400
@@ -0,0 +1,81 @@
+<tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+
+    <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description>
+
+    <macros>
+        <import>macros_last.xml</import>
+    </macros>
+
+    <requirements>
+        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        #if $db_opts.db_opts_input == 'lastdb'
+            ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
+        #end if
+
+        last-split
+
+        -f $output_format
+        #if $db_opts.db_opts_input == 'db'
+            -g '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
+        #else if $db_opts.db_opts_input == 'lastdb'
+            -g 'db_files/lastdb'
+        #end if
+
+        -d $lastsplit_opt.d
+        -c $lastsplit_opt.c
+        -t $lastsplit_opt.t
+        -M $lastsplit_opt.M
+        -S $lastsplit_opt.S
+        -m $lastsplit_opt.m
+        $lastsplit_opt.no_split
+        -b \${GALAXY_MEMORY_MB:-2G}
+
+        '$last_align'
+
+        >'$outfile'
+    ]]></command>
+
+    <inputs>
+        <expand macro="input_db" />
+        <param name="last_align" type="data" format="maf" label="LASTal data file" />
+        <param name="output_format" argument="-f" type="select" multiple="false" label="Output format">
+            <option value="MAF">MAF</option>
+            <option value="MAF+" selected="true">MAF+</option>
+        </param>
+        <section name="lastsplit_opt" title="Last-split options" expanded="false">
+            <param argument="-d" type="select" multiple="false" label="RNA direction">
+                <option value="0">Reverse</option>
+                <option value="1" selected="true">Forward</option>
+                <option value="2">Mixed</option>
+            </param>    
+            <param argument="-c" type="float" value="0.004" label="Cis-splice probability per base"/>
+            <param argument="-t" type="float" value="0.00001" label="Trans-splice probability per base"/>
+            <param argument="-M" type="float" value="7" label="Mean of ln[intron length]"/>
+            <param argument="-S" type="float" value="1.7" label="Standard deviation of ln[intron length]"/>
+            <param argument="-m" type="float" value="1" label="Maximum mismap probability"/>
+            <!--<param name="score" argument="-s" type="int" value="lastal e" label="Minimum alignement score"/>-->
+            <param name="no_split" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Write original, not split, alignement."/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="maf" label="LAST split from  ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <conditional name="db_opts">
+                <param name="db_opts_input" value="db"/>
+                <param name="database" value="humdb"/>
+            </conditional>
+            <param name="last_align" ftype="maf" value="last_align_gen.maf"/>
+            <output name="outfile" ftype="maf" file="last_split.maf"/>
+        </test>
+    </tests>
+
+    <help>@LAST_HELP@</help>
+    <citations><expand macro="citations"/></citations>
+</tool>