Mercurial > repos > greg > ks_distribution

changeset 8:1650842a90ba draft

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Uploaded
author greg
date Thu, 08 Jun 2017 10:32:44 -0400
parents 22cae2172406
children 214e2710c51e
files components.tabular kaks_input1.tabular ks_distribution.xml macros.xml output.pdf test-data/components.tabular test-data/kaks_input1.tabular test-data/output.pdf
diffstat 8 files changed, 71 insertions(+), 73 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/components.tabular	Thu Jun 08 10:32:44 2017 -0400
@@ -0,0 +1,2 @@
+species	n	number_comp	lnL	AIC	BIC	mean	variance	porportion
+species1	3	1	-3.4750	6.95	6.95	3.1183	5.7732	1.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kaks_input1.tabular	Thu Jun 08 10:32:44 2017 -0400
@@ -0,0 +1,4 @@
+SEQ1	SEQ2	Ka	Ks	Ka\Ks
+contig_241;	contig_241	1.5312	7.1619	0.2138
+contig_300	contig_300;	0.8653	3.7872	0.2285
+contig_586	contig_586;	1.7791	1.1181	1.5912
--- a/ks_distribution.xml	Tue Jun 06 09:02:08 2017 -0400
+++ b/ks_distribution.xml	Thu Jun 08 10:32:44 2017 -0400
@@ -4,14 +4,12 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements_ks_distribution" />
-    <command detect_errors="exit_code">
-        <![CDATA[
-            Rscript $__tool_directory__/ks_distribution.R
-            -k '$input'
-            -c '$components'
-            -o '$output'
-        ]]>
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript $__tool_directory__/ks_distribution.R
+-k '$input'
+-c '$components'
+-o '$output'
+    ]]></command>
     <inputs>
         <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
         <param name="components" format="tabular" type="data" label="Significant components" />
--- a/macros.xml	Tue Jun 06 09:02:08 2017 -0400
+++ b/macros.xml	Thu Jun 08 10:32:44 2017 -0400
@@ -1,29 +1,29 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <token name="@WRAPPER_VERSION@">0.8</token>
+    <token name="@WRAPPER_VERSION@">1.0</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_aligner">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_classifier">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_integrator">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement>
         </requirements>
     </xml>
     <xml name="requirements_kaks_analysis">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement>
         </requirements>
     </xml>
     <xml name="requirements_ks_distribution">
@@ -33,7 +33,7 @@
     </xml>
     <xml name="requirements_gene_family_phylogeny_builder">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_phylogeny_builder</requirement>
         </requirements>
     </xml>
     <xml name="param_codon_alignments">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/output.pdf	Thu Jun 08 10:32:44 2017 -0400
@@ -0,0 +1,52 @@
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--- a/test-data/components.tabular	Tue Jun 06 09:02:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-species	n	number_comp	lnL	AIC	BIC	mean	variance	porportion
-species1	3	1	-3.4750	6.95	6.95	3.1183	5.7732	1.00
--- a/test-data/kaks_input1.tabular	Tue Jun 06 09:02:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
-contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912
--- a/test-data/output.pdf	Tue Jun 06 09:02:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
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