Mercurial > repos > jjjjia > cpo_prediction

changeset 5:698579246d0d draft

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planemo upload
author jjjjia
date Tue, 21 Aug 2018 17:53:08 -0400
parents bd6f5844d60e
children cabceaa239e4
files cpo_clustalw.xml cpo_galaxy_prediction.py cpo_galaxy_predictions.xml cpo_galaxy_tree.xml cpo_mlst.xml cpo_mobsuite.xml cpo_resfinder.xml cpo_rgi.xml cpo_snippy.xml cpo_snpdist.xml
diffstat 10 files changed, 35 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/cpo_clustalw.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_clustalw.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
-  <description>makes tree from alignment</description>
+  <description>Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment</description>
   <requirements>
      <requirement type="package" version="2.1">clustalw</requirement>
   </requirements>   
@@ -15,21 +15,6 @@
     <data name="phylip" format="txt" from_work_dir="*.ph"/> 
     <data name="njtree" format="txt" from_work_dir="*.nj*"/>
   </outputs>
-  <tests>
-    <test>
-        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
-        <section name="adv_param">
-         <param name="evalue" value="0.00001"/>
-         <param name="unicycler_contigs" value="True"/>
-         <param name="run_circlator"  value="True"/>
-        </section>
-        <output name="outfile1">
-          <assert_contents>
-            <has_text text="NC_019097"/>
-          </assert_contents>  
-        </output> 
-    </test>
-  </tests>
   <help>
 
 **Syntax**
@@ -64,4 +49,4 @@
   url = {https://github.com/phac-nml/mob-suite}
     }</citation>
   </citations>
-</tool>
\ No newline at end of file
+</tool>
--- a/cpo_galaxy_prediction.py	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_prediction.py	Tue Aug 21 17:53:08 2018 -0400
@@ -26,7 +26,7 @@
 import numpy
 
 
-debug = False #True #debug skips the shell scripts and also dump out a ton of debugging messages
+debug = True #debug skips the shell scripts and also dump out a ton of debugging messages
 
 if not debug:
     #parses some parameters
@@ -645,4 +645,4 @@
 Main()
 
 end = time.time()
-print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
+print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
\ No newline at end of file
--- a/cpo_galaxy_predictions.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_predictions.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="cpo_prediction" name="cpoParser" version="0.1.0">
-	<description>this tool parses stuff</description>
-	<requirements>
+<tool id="cpo_prediction_parser" name="cpo_prediction_parser" version="0.1.0">
+  <description>This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow</description>
+  <requirements>
 		<requirement type="package" version="0.23.4">pandas</requirement>
 		<requirement type="package" version="3.6">python</requirement>
 	</requirements>
@@ -19,18 +19,18 @@
     ]]>
 	</command>
     <inputs>
-        <param type="text" name="ID"/>
+        <param type="txt" name="ID"/>
         <param type="data" name="mlst" format="tabular" />
         <param type="data" name="mobsuitecontig" format="tabular" />
         <param type="data" name="mobsuiteaggregate" format="tabular" />
         <param type="data" name="abricate" format="tabular" />
         <param type="data" name="rgi" format="tabular" />
         <param type="data" name="plasmidfinder" format="tabular" />
-        <param type="text" name="expected"/>
+        <param type="txt" name="expected"/>
     </inputs>
     <outputs>
         <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
-		  <data name="txtSummary" format="text" from_work_dir="summary.txt"/>
+		  <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
     </outputs>
 	<tests>
         <test>
--- a/cpo_galaxy_tree.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_galaxy_tree.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,9 +1,10 @@
-<tool id="cpo_tree_galaxy" name="cpoTree" version="0.1.0">
-	<description>this tool makes tree</description>
+<tool id="cpo_tree_drawer" name="cpo_tree_drawer" version="0.1.0">
+	<description>This tool makes a phylogenetic tree using data from snippy alignments, clustalw NJ tree and metadat from cpo_prediction workflow using ETE3</description>
 	<requirements>
 		<requirement type="package" version="0.23.4">pandas</requirement>
 		<requirement type="package" version="3.6">python</requirement>
-	</requirements>
+    <requirement type="package" version="3.1.1">ete3</requirement>
+  </requirements>
 	<command detect_errors="exit_code">
     <![CDATA[
 	    python '$__tool_directory__/cpo_galaxy_tree.py'
--- a/cpo_mlst.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_mlst.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,6 @@
-<tool id="mlst" name="MLST" version="2.11">
-    <requirements>
+<tool id="cpo_mlst" name="cpo_mlst" version="2.11">
+  <description>Modified MLST v2.11 to support for the cpo_prediction workflow</description>
+  <requirements>
         <requirement type="package" version="2.11">mlst</requirement>
     </requirements>
 
--- a/cpo_mobsuite.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_mobsuite.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
-<tool id="mob_recon" name="MOB-Recon" version="1.4.8">
-  <description>Type contigs and extract plasmid sequences</description>
+<tool id="cpo_mob_recon" name="cpo_mob_recon" version="1.4.8">
+  <description>Modified Mobsuite (Mob-Recon) v1.4.8 to add the mob_typer for the cpo_prediction workflow</description>
   <requirements>
      <requirement type="package" version="1.4.8">mob_suite</requirement>
   </requirements>   
--- a/cpo_resfinder.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_resfinder.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,5 @@
-<tool id="resfindercpo" name="resfindercpo" version="0.8">
-	<description>this tool parses stuff</description>
+<tool id="cpo_resfinder" name="cpo_resfinder" version="0.8">
+	<description>Modified version of Resfinder 0.8 to use custom carbapenamase database</description>
 	<requirements>
 		<requirement type="package" version="0.8">abricate</requirement>
 	</requirements>
--- a/cpo_rgi.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_rgi.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,5 +1,6 @@
-<tool id="rgi" name="rgi" version="4.0.3">
-    <requirements>
+<tool id="cpo_rgi" name="cpo_rgi" version="4.0.3">
+  <description>Modified version of RGI to make it support galaxy without using a datatable by using the --local flag</description>
+  <requirements>
         <requirement type="package" version="4.0.3">rgi</requirement>
 		<requirement type="package" version="2.7">python</requirement>
     </requirements>
--- a/cpo_snippy.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_snippy.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,4 +1,5 @@
-<tool id="snippy" name="snippy" version="3.2">
+<tool id="cpo_snippy" name="CPO_Snippy" version="3.2">
+  <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description>
   <requirements>
     <requirement type="package" version="3.2">snippy</requirement>
   </requirements>
@@ -32,7 +33,11 @@
 
       &&
 
-      tar -czf out.tgz out
+      #import re
+      #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
+      mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+
+      tar -czf out.tgz ${dir_name}
 
 
     ]]>
--- a/cpo_snpdist.xml	Mon Aug 20 19:31:34 2018 -0400
+++ b/cpo_snpdist.xml	Tue Aug 21 17:53:08 2018 -0400
@@ -1,6 +1,7 @@
-<tool id="snippy-dist" name="snippy-dist" version="4.0.2">
-    <requirements>
-        <requirement type="package" version="4.0.2">snippy</requirement>
+<tool id="cpo_snippy_dist" name="cpo_snippy_dist" version="0.6">
+  <description>modified snippy-dist v0.6 to the tree drawer of the cpo_predictions workflow</description>
+  <requirements>
+        <requirement type="package" version="0.6">snp-dists</requirement>
     </requirements>
     <command detect_errors="exit_code">
       <![CDATA[