Mercurial > repos > rdvelazquez > hyphy_sm19

changeset 4:65816621ff9f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:22:23 -0400
parents e2e7e6a88b0f
children
files hyphy_sm19.xml macros.xml
diffstat 2 files changed, 80 insertions(+), 94 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_sm19.xml	Thu Mar 21 06:08:38 2019 -0400
+++ b/hyphy_sm19.xml	Fri Jun 07 10:22:23 2019 -0400
@@ -1,15 +1,11 @@
 <?xml version="1.0"?>
-<tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0">
-    <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <requirements>
-        <requirement type="package" version="2.4.0">hyphy</requirement>
-    </requirements>
-    <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
+<tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.5.0+galaxy0">
+  <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
     #set $count = len($partitions)
     ln -s '$input_file' sm19_input.nhx &&
     @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
@@ -19,67 +15,64 @@
         '${partition.regex}'
     #end for
     $replicates
-    ]]>
-    </command>
-    <inputs>
-        <param name="input_file" type="data" format="nhx" label="Input tree" />
-        <repeat name="partitions" min="2" max="50" title="Partitions">
-            <param name="label" type="text" label="Partition label" />
-            <param name="regex" type="text" label="Regular expression">
-                <sanitizer>
-                    <valid initial="string.printable">
-                        <remove value="&apos;" />
-                    </valid>
-                    <mapping initial="none">
-                        <add source="&apos;" target="__sq__" />
-                    </mapping>
-                </sanitizer>
-            </param>
-        </repeat>
-        <param name="replicates" type="integer" min="1" max="1000000" value="100" />
-    </inputs>
-    <outputs>
-        <data name="sm19_output" format="hyphy_json_results" from_work_dir="sm19_input.nhx.json" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_file" ftype="fasta" value="sm19-in1.nhx" />
-            <param name="replicates" value="1000" />
-            <repeat name="partitions">
-                <param name="label" value="Blood" />
-                <param name="regex" value="B[0-9]+"/>
-            </repeat>
-            <repeat name="partitions">
-                <param name="label" value="Semen" />
-                <param name="regex" value="S[0-9]+"/>
-            </repeat>
-            <output name="sm19_output" file="sm19-out1.json" compare="sim_size" />
-        </test>
-        <test>
-            <param name="input_file" ftype="fasta" value="sm19-in2.nhx" />
-            <param name="replicates" value="1000" />
-            <repeat name="partitions">
-                <param name="label" value="Blood" />
-                <param name="regex" value="B[0-9]+"/>
-            </repeat>
-            <repeat name="partitions">
-                <param name="label" value="Semen" />
-                <param name="regex" value="S[0-9]+"/>
-            </repeat>
-            <output name="sm19_output" file="sm19-out2.json" compare="sim_size" />
-        </test>
-    </tests>
-    <help>
-        <![CDATA[
+    ]]></command>
+  <inputs>
+    <param name="input_file" type="data" format="nhx" label="Input tree"/>
+    <repeat name="partitions" min="2" max="50" title="Partitions">
+      <param name="label" type="text" label="Partition label"/>
+      <param name="regex" type="text" label="Regular expression">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+          </valid>
+          <mapping initial="none">
+            <add source="'" target="__sq__"/>
+          </mapping>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
+  </inputs>
+  <outputs>
+    <data name="sm19_output" format="hyphy_json_results" from_work_dir="sm19_input.nhx.json"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
+      <param name="replicates" value="1000"/>
+      <repeat name="partitions">
+        <param name="label" value="Blood"/>
+        <param name="regex" value="B[0-9]+"/>
+      </repeat>
+      <repeat name="partitions">
+        <param name="label" value="Semen"/>
+        <param name="regex" value="S[0-9]+"/>
+      </repeat>
+      <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
+      <param name="replicates" value="1000"/>
+      <repeat name="partitions">
+        <param name="label" value="Blood"/>
+        <param name="regex" value="B[0-9]+"/>
+      </repeat>
+      <repeat name="partitions">
+        <param name="label" value="Semen"/>
+        <param name="regex" value="S[0-9]+"/>
+      </repeat>
+      <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
 This analysis implements canonical and modified versions of the Slatkin-Maddison
 phylogeny based test for population segregation. The test estimates the minimum
 number of migration events using maximum parsimony, and then evaluating whether
 or not this number is lower than expected in a panmictic or unstructured
 population using permutation tests.
-        ]]>
-    </help>
-    <expand macro="citations">
-        <citation type="bibtex">
+        ]]></help>
+  <expand macro="citations">
+    <citation type="bibtex">
             @UNPUBLISHED{slatkin,
                 author = "Slatkin M, Maddison WP",
                 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
@@ -87,5 +80,5 @@
                 note = "Genetics 123(3):603-613",
                 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
         </citation>
-    </expand>
+  </expand>
 </tool>
--- a/macros.xml	Thu Mar 21 06:08:38 2019 -0400
+++ b/macros.xml	Fri Jun 07 10:22:23 2019 -0400
@@ -6,50 +6,43 @@
   </xml>
   <xml name="gencode">
     <param name="gencodeid" type="select" label="Genetic code">
-      <option value="1">Universal code</option>
-      <option value="2">Vertebrate mitochondrial DNA code</option>
-      <option value="3">Yeast mitochondrial DNA code</option>
-      <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
-      <option value="5">Invertebrate mitochondrial DNA code</option>
-      <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
-      <option value="7">Echinoderm mitochondrial DNA code</option>
-      <option value="8">Euplotid Nuclear code</option>
-      <option value="9">Alternative Yeast Nuclear code</option>
-      <option value="10">Ascidian mitochondrial DNA code</option>
-      <option value="11">Flatworm mitochondrial DNA code</option>
-      <option value="12">Blepharisma Nuclear code</option>
+      <option value="Universal">Universal code</option>
+      <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option>
+      <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option>
+      <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
+      <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option>
+      <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
+      <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option>
+      <option value="Euplotid-Nuclear">Euplotid Nuclear code</option>
+      <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option>
+      <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option>
+      <option value="Flatworm-mtDNA,">Flatworm mitochondrial DNA code</option>
+      <option value="Blepharisma-Nuclear">Blepharisma Nuclear code</option>
     </param>
   </xml>
   <xml name="branches">
     <param name="branches" type="select" label="Set of branches to test">
-      <option value="1">All branches</option>
-      <option value="2">Internal branches</option>
-      <option value="3">Leaf branches</option>
-      <option value="4">Unlabeled branches</option>
+      <option value="All">All branches</option>
+      <option value="Internal">Internal branches</option>
+      <option value="Leaves">Leaf branches</option>
+      <option value="'Unlabeled-branches'">Unlabeled branches</option>
     </param>
   </xml>
-  <xml name="version_command">
-    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
-  </xml>
   <xml name="citations">
     <citations>
       <citation type="doi">10.1093/bioinformatics/bti079</citation>
       <yield/>
     </citations>
   </xml>
-  <token name="@VERSION@">2.3.14</token>
+  <token name="@VERSION@">2.5.0</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">hyphy</requirement>
       <yield/>
     </requirements>
   </xml>
-  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
+  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
-  <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
-  <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
-export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
-export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
-cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
+  <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | hyphy LIBPATH=\$HYPHY_LIB ]]></token>
 </macros>