diff swift.xml @ 0:0802a40af216 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ commit 2d4c604c2e76baaf744748be3d56e5504a0184b7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/swift.xml	Sat Dec 09 17:37:03 2017 -0500
@@ -0,0 +1,135 @@
+<tool id="swiftlink" name="Swiftlink" version="@VERSION@.0" >
+    <description>Parallel MCMC Linkage Analysis</description>
+    <macros>
+        <token name="@VERSION@">1.0</token>
+        <xml name="test_inputs" >
+            <param name="inp_ped" value="pedin.21" />
+            <param name="inp_dat" value="datain.21" />
+            <param name="inp_map" value="map.21" />
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">swiftlink</requirement>
+        <requirement type="package" version="2017.3">linkage2allegro</requirement>
+    </requirements>
+    <!-- <version_command></version_command> Note: a version is never output by the program... -->
+    <command detect_errors='exit_code'><![CDATA[
+swiftlink
+ -p '${inp_ped}'
+ -m '${inp_map}'
+ -d '${inp_dat}'
+ ${misc.X}
+ ${misc.a}
+ -q ${misc.q}
+ -c \${GALAXY_SLOTS:-3}
+ -i ${mcmc.i}
+ -b ${mcmc.b}
+ -s ${mcmc.s}
+ -x ${mcmc.x}
+ -l ${mcmc.l}
+ -n ${mcmc.n}
+ -R ${mcmc.R}
+
+#if $misc.r
+    -r '${misc.r}'
+#end if
+
+#if $elod_opts.e == 'yes':   ## 'true' / 'false' as opt values parse badly
+    -e
+    -f $elod_opts.f
+    -w $elod_opts.w
+    -k '$elod_opts.k'
+    -u $elod_opts.u 2> ${out_elod}   ## stderr and stdout switched for some reason...
+#else
+    -o swiftlink.out
+    && linkage2allegro '${inp_ped}' '${inp_map}' swiftlink -l swiftlink.out
+    && mv linkage.allegro_lod '${out_fparam}'
+#end if
+
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
+        <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." />
+        <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" />
+
+        <conditional name="elod_opts" >
+            <param argument="-e" type="select" label="Calculate Expected LOD scores from pedigree only.">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes" >
+                <param name="f" argument="-f" type="float" min="0" max="0.99" value="0.0001" label="Frequency" />
+                <param name="w" argument="-w" type="float" min="0" max="1" value="0.5" label="Seperation" />
+                <param name="k" argument="-k" type="text" value="0.00,0.00,1.00" label="Penetrance List" />
+                <param name="u" argument="-u" type="integer" min="1" value="1000000" label="Replicates" />
+            </when>
+            <when value="no" ></when>
+        </conditional>
+
+        <section name="mcmc" title="Marko Chain Monte Carlo (MCMC) Options" expanded="false" >
+            <param argument="-i" type="integer" min="1" value="50000" label="Iterations" />
+            <param argument="-b" type="integer" min="1" value="50000" label="Burn-ins" />
+            <param argument="-s" type="integer" min="1" value="1000" label="Sequential Imputation" />
+            <param argument="-x" type="integer" min="1" value="10" label="Scoring Period" />
+            <param argument="-n" type="integer" min="1" value="5" label="Lod Scores" />
+            <param argument="-R" type="integer" min="1" value="1" label="Runs" />
+            <param argument="-l" type="float" min="0" max="1" value="0.5" label="L-Sampler Probability" />
+        </section>
+
+        <section name="misc" title="Miscellaneous" expanded="true" >
+            <param argument="-X" type="boolean" truevalue="-X" falsevalue="" value="false" label="X-linked"/>
+            <param argument="-a" type="boolean" truevalue="-a" falsevalue="" value="false" label="Affecteds only"/>
+            <param argument="-q" type="integer" min="1" value="1000000" label="Peel-sequence Iterator"/>
+            <param argument="-r" type="data" format="txt" label="Random seeds (single-column)" optional="true" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage File" >
+            <filter>elod_opts['e'] == "no"</filter>
+        </data>
+        <data name="out_elod" format="txt" label="${tool.name} on ${on_string}: Elod score" >
+            <filter>elod_opts['e'] == "yes"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_inputs" />
+
+            <param name="b" value="1000" />
+            <param name="i" value="2000" />
+            <param name="x" value="150" />
+            <param name="e" value="yes" />
+            <param name="u" value="1000" />
+
+            <output name="out_elod" >
+                <assert_contents>
+                    <has_text_matching expression='sex-linked = false' />
+                    <has_text_matching expression='Total\s+\|\s+\d+\.\d+\s*' />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <expand macro="test_inputs" />
+
+            <param name="b" value="5000" />
+            <param name="i" value="100" />
+            <param name="x" value="100" />
+
+            <output name="out_fparam" >
+                <assert_contents>
+                    <has_text_matching expression="(\s+-?\d+\.\d+){4}\s+rs468601" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees. The current version of SwiftLink only supports SNP markers.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts704</citation>
+    </citations>
+</tool>