# HG changeset patch
# User amos
# Date 1489779293 14400
# Node ID 259d81207224721f9e7b6e2d0d3e336938714f51
# Parent  679b084023adb6a9e8626081b766388cb4161973
planemo upload for repository https://github.com/arpcard/rgi_conda_dev commit 235d3fe73ff63b485954f184e0a5a4cdb1c7338f

diff -r 679b084023ad -r 259d81207224 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,5 @@
+# RGI wrapper
+
+This wrapper is used to run Resistance Gene Identifier - Version 3.1.2 on galaxy environment.
+
+This tool is used together with data manager for RGI: rgi_database_builder.
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 Report.json
diff -r 679b084023ad -r 259d81207224 card.json
diff -r 679b084023ad -r 259d81207224 dataSummary.txt
diff -r 679b084023ad -r 259d81207224 init_dir/INSTALL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/INSTALL	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,29 @@
+# Run init to geenerate all xml files
+$ ./init
+
+OR 
+
+# Run init_rgi to generate rgi.xml
+$ ./init_rgi
+
+# Run init_clean to generate clean.xml
+$ ./init_clean
+
+
+# Run init_tab to generate tab.xml
+$ ./init_tab
+
+
+# Run init_load to generate load.xml
+$ ./init_load
+
+# add update GALAXY_SLOTS
+
+\${GALAXY_SLOTS:-Z}
+
+Z is the defaul value
+
+Example: For number of threads for RGI
+
+\${GALAXY_SLOTS:-32}
+
diff -r 679b084023ad -r 259d81207224 init_dir/clean
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/clean	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,6 @@
+rm -r test-data
+rm *.xml
+rm *.json
+rm *.txt
+rm data*
+source deactivate
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/init
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/init	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,14 @@
+echo "========================================[info] adding files =================================================== "
+touch dataSummary.txt
+touch Report.json
+wget https://card.mcmaster.ca/latest/data
+tar xvjf data card.json
+echo "========================================[info] initializing rgi tool =================================================== "
+./init_rgi
+echo "========================================[info] initializing rgi_jsontab tool =================================================== "
+./init_tab
+echo "========================================[info] initializing rgi_clean tool =================================================== "
+./init_clean
+echo "========================================[info] initializing rgi_load tool =================================================== "
+./init_load
+echo "========================================[info] Done. =================================================== "
diff -r 679b084023ad -r 259d81207224 init_dir/init_clean
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/init_clean	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,10 @@
+planemo tool_init \
+--force \
+--id 'rgi_clean' \
+--name 'Resistance Gene Identifier (RGI) - Cleans BLAST databases' \
+--version '3.1.2' \
+--description 'This tool cleans BLAST databases used by RGI' \
+--help_from_command 'rgi_clean -h ' \
+--test_case \
+--example_command 'rgi_clean' \
+--cite_url 'https://card.mcmaster.ca/about'
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/init_load
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/init_load	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,12 @@
+planemo tool_init \
+--force \
+--id 'rgi_load' \
+--name 'Resistance Gene Identifier (RGI) - Loads new CARD data into RGI tool' \
+--version '3.1.2' \
+--description 'This tool loads new CARD data into RGI tool' \
+--help_from_command 'rgi_load -h ' \
+--input 'card.json' \
+--test_case \
+--example_command 'rgi_load -i card.json' \
+--example_input 'card.json' \
+--cite_url 'https://card.mcmaster.ca/about'
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/init_rgi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/init_rgi	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,18 @@
+planemo tool_init \
+--force \
+--id 'rgi' \
+--name 'Resistance Gene Identifier (RGI)' \
+--version '3.1.2' \
+--description 'This tool predict resistome(s) from protein or nucleotide data based on homology and SNP models' \
+--requirement python@2.7 \
+--requirement biopython@1.68 \
+--requirement six@1.9.0 \
+--requirement prodigal@2.6.3 \
+--requirement diamond@0.8.36 \
+--requirement zlib@1.2.8 \
+--help_from_command 'rgi -h ' \
+--command 'rgi --input_sequence $input_sequence --input_type $input_type --out_file $output1 --num_threads "\${GALAXY_SLOTS:-32}"  --verbose $verbose --alignment_tool $alignment_tool' \
+--input 'sequence.fasta' \
+--output 'sequence.fasta.output' \
+--named_output 'Report.json' \
+--cite_url 'https://card.mcmaster.ca/about'
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/init_tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/init_tab	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,14 @@
+planemo tool_init \
+--force \
+--id 'rgi_jsontab' \
+--name 'Resistance Gene Identifier (RGI) - Convert RGI JSON to Tab-delimited' \
+--version '3.1.2' \
+--description 'This tool converts RGI json output file to tab-demited output' \
+--help_from_command 'rgi_jsontab -h ' \
+--input 'Report.json' \
+--output 'dataSummary.txt' \
+--test_case \
+--example_command 'rgi_jsontab -i Report.json -o dataSummary.txt' \
+--example_input 'Report.json' \
+--example_output 'dataSummary.txt' \
+--cite_url 'https://card.mcmaster.ca/about'
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/run
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/run	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,1 @@
+planemo s --conda_auto_install --conda_auto_init --conda_dependency_resolution
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 init_dir/run2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/init_dir/run2	Fri Mar 17 15:34:53 2017 -0400
@@ -0,0 +1,16 @@
+# create virtual env
+touch /Users/amos/.planemo/gx_venv/bin/activate
+# activate the virtual env
+source /Users/amos/.planemo/gx_venv/bin/activate
+planemo l \
+rgi.xml \
+--report_level all \
+--report_xunit ./galaxy
+planemo t \
+--conda_debug \
+--failed \
+--conda_auto_init 
+planemo s
+
+
+planemo s --conda_auto_install --conda_auto_init --conda_dependency_resolution
\ No newline at end of file
diff -r 679b084023ad -r 259d81207224 rgi.xml
--- a/rgi.xml	Fri Oct 14 14:28:52 2016 -0400
+++ b/rgi.xml	Fri Mar 17 15:34:53 2017 -0400
@@ -1,93 +1,65 @@
-<tool id="rgi" name="RGI" version="3.1.1">
-    <description>This tool provides detection of antibiotic resistance associated genes.</description>
+<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="3.1.2">
+    <description>This tool predict resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
     <requirements>
-        <requirement type="package">python</requirement>
-        <requirement type="package">biopython</requirement>
-        <requirement type="package">six</requirement>
-        <requirement type="package">zlib</requirement>
-        <requirement type="package">rgi</requirement>
-        <requirement type="package">prodigal</requirement>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="1.68">biopython</requirement>
+        <requirement type="package" version="1.9.0">six</requirement>
+        <requirement type="package" version="2.6.3">prodigal</requirement>
+        <requirement type="package" version=">=0.8.24">diamond</requirement>
+        <requirement type="package" version="1.2.8">zlib</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        rgi -i $inputSeq -t $inType -x $orf -c $clean -e $exclude_loose -n $num_threads -o Report
+        rgi --input_sequence $input_sequence --input_type $input_type --output_file Report --num_threads "\${GALAXY_SLOTS:-32}"  --verbose $verbose --alignment_tool $alignment_tool --loose_criteria $loose_criteria --clean $clean --db "${__tool_data_path__}/rgi_databases/$rgi_databases"
     ]]></command>
     <inputs>
 
-        <param type="select" name="inType" label="Input type" multiple="false">
-          <option value="contig">contig (Nucluotides Sequence)</option>
-          <option value="protein" selected="true">protein (Protein Sequence)</option>
-          <option value="read">read (Metagenomics Sequence / FastQ)</option>
+        <param type="data" name="input_sequence" format="fastq,fasta" label="Input Sequence" />
+
+        <param type="select" name="input_type"  label="Input Type" multiple="false">
+            <option value="contig" selected="true">CONTIG (Nucluotides Sequence)</option>
+            <option value="protein">PROTEIN (Protein Sequence)</option>
+            <option value="read">READ (Metagenomics Sequence / FastQ)</option>
         </param>
-              
-        <param type="data" name="inputSeq" format="fastq,fasta" label="Input Sequence" />
 
-        <param type="integer" name="num_threads" format="fasta" label="THREADS" value="8" min="8" max="64" />
-
-        <param type="select" name="exclude_loose" label="CRITERIA" multiple="false">
-          <option value="0" selected="true">NO</option>
-          <option value="1">YES</option>
+        <param type="select" name="alignment_tool"  label="Alignment Tool">
+            <option value="blast" selected="true">BLAST</option>
+            <option value="diamond">DIAMOND</option>
         </param>
 
-        <param type="select" name="clean" label="CLEAN" multiple="false">
-          <option value="0" selected="true">NO</option>
-          <option value="1">YES</option>
+        <param type="select" name="verbose"  label="Log progress to file (VERBOSE)" multiple="false">
+            <option value="off" selected="true">OFF</option>
+            <option value="on">ON</option>
+        </param>
+
+        <param type="select" name="clean"  label="Remove temporary files (CLEAN)" multiple="false">
+            <option value="yes" selected="true">YES</option>
+            <option value="no">NO</option>
         </param>
 
-        <param type="select" name="verbose" label="VERBOSE" multiple="false">
-          <option value="0" selected="true">NO</option>
-          <option value="1">YES</option>
+        <param type="select" name="loose_criteria" label="Exclude loose hits (CRITERIA)" multiple="false">
+          <option value="yes">YES</option>
+          <option value="no" selected="true">NO</option>
         </param>
 
-        <param type="select" name="orf" label="ORF Finder" multiple="false">
-          <option value="0" selected="true">Prodigal</option>
-          <option value="1">GeneMark</option>
+        <param label="Select a RGI database" name="rgi_databases" type="select">
+            <options from_data_table="rgi_databases">
+                <validator message="No databases are available built-in" type="no_options" />
+            </options>
         </param>
 
-        <!--<param type="data" name="version" label="Version Number"/>-->
-
     </inputs>
-    <outputs>    
-      <!--
-        <data format="json" name="Report" from_work_dir="Report.json" label="RGI: Output (JSON)" />
-        <data format="fasta" name="protein.contig.fsa"  label="RGI: ORFs Protein (FASTA)" >
-          <filter>inType == "contig"</filter>
-          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fsa" format="fasta" />
+  
+    <outputs>
+        <data format="json" name="Report" from_work_dir="Report.json" label="${tool.name} on ${on_string}: (JSON)" />
+        <data format="tabular" name="Summary" from_work_dir="Report.txt" label="${tool.name} on ${on_string}: (TXT)" />
+        <data format="gff3" name="gff" from_work_dir="Report.gff3" label="${tool.name} on ${on_string}: (GFF3)" >
+            <filter>(input_type == 'contig')</filter>
         </data>
-
-        <data format="fasta" name="nucleotide.contigToORF.fsa"  label="RGI: ORFs - Nucleotide (FASTA)" >
-          <filter>inType == "contig"</filter>
-          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fsa" format="fasta" />
-        </data>
-      <collection name="split_output" type="list" label="Table split on first column">
-          <discover_datasets pattern="__name_and_ext__" directory="outputs" />
-      </collection>
-    -->
-     <!--
-    <data format="json" name="Report" from_work_dir="Report.json" label="RGI: Output (JSON)" />
+    </outputs>  
 
-    <data format="fsa" name="Other">
-      <filter>inType == "contig"</filter>
-      <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fsa" format="fasta" visible="true" label="RGI: ORFs (FASTA)"/>
-    </data>
-  -->
-
-  <data format="json" name="Report" from_work_dir="Report.json" label="RGI: Output (JSON)" />
-<!--
-  <data format="fsa" name="orfs" >
-    <filter>inType == "contig"</filter>
-    <discover_datasets pattern="(?P&lt;name&gt;.+)\.fsa" format="fasta" visible="true" label="RGI: ORFs (FASTA)" />
-    <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fsa" format="fasta" visible="true"/>
-  </data>
-
-  <data format="xml" name="blastResult" >
-    <discover_datasets pattern="(?P&lt;name&gt;.+)\.xml" format="xml" visible="true" label="RGI: BLAST (XML)"/>
-  </data>
--->
-    </outputs>
-  
     <tests>
         <test>
             <param name="inType" value="protein"/>
@@ -95,41 +67,48 @@
             <output name="Report" file="Report.json"/>
         </test>
     </tests>
-  
     <help><![CDATA[
+
         usage: rgi [-h] [-t INTYPE] [-i INPUTSEQ] [-n THREADS] [-o OUTPUT]
-           [-e CRITERIA] [-c CLEAN] [-d DATA] [-v VERBOSE] [-x ORF] [-V]
+                      [-e CRITERIA] [-c CLEAN] [-d DATA] [-l VERBOSE] [-a ALIGNER]
+                      [-r DATABASE] [-sv] [-dv]
 
-Resistance Gene Identifier - Version 3.1.1
+        Resistance Gene Identifier - Version 3.1.2
 
-optional arguments:
-  -h, --help            show this help message and exit
-  -t INTYPE, --inType INTYPE
-                        must be one of contig, orf, protein, read (default:
-                        contig)
-  -i INPUTSEQ, --inputSeq INPUTSEQ
-                        input file must be in either FASTA (contig and
-                        protein), FASTQ(read) or gzip format! e.g
-                        myFile.fasta, myFasta.fasta.gz
-  -n THREADS, --num_threads THREADS
-                        Number of threads (CPUs) to use in the BLAST search
-                        (default=32)
-  -o OUTPUT, --out_file OUTPUT
-                        Output JSON file (default=Report)
-  -e CRITERIA, --exclude_loose CRITERIA
-                        This option is used to include or exclude the loose
-                        hits. Options are 0 or 1 (default=1 for exclude)
-  -c CLEAN, --clean CLEAN
-                        This removes temporary files in the results directory
-                        after run. Options are 0 or 1 (default=1 for remove)
-  -d DATA, --data DATA  Specify a data-type, i.e. wgs, chromosome, plasmid,
-                        etc. (default = NA)
-  -v VERBOSE, --verbose VERBOSE
-                        log process to file. Options are 0 or 1 (default = 0
-                        for no logging)
-  -x ORF, --orf ORF     choose between prodigal and MetaGeneMark orf finder.
-                        Options are 0 or 1 (default = 0 for using prodigal)
-  -V, --version         Prints version number
+        optional arguments:
+          -h, --help            show this help message and exit
+          -t INTYPE, --input_type INTYPE
+                                must be one of contig, orf, protein, read (default:
+                                contig)
+          -i INPUTSEQ, --input_sequence INPUTSEQ
+                                input file must be in either FASTA (contig and
+                                protein), FASTQ(read) or gzip format! e.g
+                                myFile.fasta, myFasta.fasta.gz
+          -n THREADS, --num_threads THREADS
+                                Number of threads (CPUs) to use in the BLAST search
+                                (default=32)
+          -o OUTPUT, --output_file OUTPUT
+                                Output JSON file (default=Report)
+          -e CRITERIA, --loose_criteria CRITERIA
+                                The options are YES to include loose hits and NO to
+                                exclude loose hits. (default=NO to exclude loose hits)
+          -c CLEAN, --clean CLEAN
+                                This removes temporary files in the results directory
+                                after run. Options are NO or YES (default=YES for
+                                remove)
+          -d DATA, --data DATA  Specify a data-type, i.e. wgs, chromosome, plasmid,
+                                etc. (default = NA)
+          -l VERBOSE, --verbose VERBOSE
+                                log progress to file. Options are OFF or ON (default =
+                                OFF for no logging)
+          -a ALIGNER, --alignment_tool ALIGNER
+                                choose between BLAST and DIAMOND. Options are BLAST or
+                                DIAMOND (default = BLAST)
+          -r DATABASE, --db DATABASE
+                                specify path to CARD blast databases (default: None)
+          -sv, --software_version
+                                Prints software number
+          -dv, --data_version   Prints data version number
 
     ]]></help>
     <citations>
diff -r 679b084023ad -r 259d81207224 rgi_clean.xml
--- a/rgi_clean.xml	Fri Oct 14 14:28:52 2016 -0400
+++ b/rgi_clean.xml	Fri Mar 17 15:34:53 2017 -0400
@@ -1,7 +1,6 @@
-<tool id="rgi_clean" name="RGI: Cleaner" version="3.1.1">
+<tool id="rgi_clean" name="Resistance Gene Identifier (RGI) - Cleans BLAST databases" version="3.1.2">
     <description>This tool cleans BLAST databases used by RGI</description>
     <requirements>
-         <requirement type="package">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -12,19 +11,19 @@
     <inputs>
     </inputs>
     <outputs>
-        <data format="txt" name="report" label="RGI Clean Report"/>
     </outputs>
     <tests>
         <test>
         </test>
     </tests>
     <help><![CDATA[
+
         usage: rgi_clean [-h]
 
-Removes BLAST databases created using card.json
+        Removes BLAST databases created using card.json
 
-optional arguments:
-  -h, --help  show this help message and exit
+        optional arguments:
+          -h, --help  show this help message and exit
 
     ]]></help>
     <citations>
diff -r 679b084023ad -r 259d81207224 rgi_jsontab.xml
--- a/rgi_jsontab.xml	Fri Oct 14 14:28:52 2016 -0400
+++ b/rgi_jsontab.xml	Fri Mar 17 15:34:53 2017 -0400
@@ -1,23 +1,20 @@
-<tool id="rgi_jsontab" name="RGI: Tabular" version="3.1.1">
+<tool id="rgi_jsontab" name="Resistance Gene Identifier (RGI) - Convert RGI JSON to Tab-delimited" version="3.1.2">
     <description>This tool converts RGI json output file to tab-demited output</description>
     <requirements>
-      <requirement type="package">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        rgi_jsontab -i $Report -x $orf -o dataSummary
+        rgi_jsontab -i "$input1" -o "$output1"
     ]]></command>
     <inputs>
         <param type="data" name="Report" format="json" />
-        <param type="select" name="orf" label="ORF Finder" multiple="false">
-          <option value="0" selected="true">Prodigal</option>
-          <option value="1">GeneMark</option>
-        </param>
+        <param type="data" name="input1" format="json" />
     </inputs>
     <outputs>
-        <data format="tabular" name="dataSummary" from_work_dir="dataSummary.txt" label="RGI: Output (Tabular)" />
+        <data name="dataSummary" format="txt" />
+        <data name="output1" format="txt" />
     </outputs>
     <tests>
         <test>
@@ -26,19 +23,21 @@
         </test>
     </tests>
     <help><![CDATA[
-        usage: rgi_jsontab [-h] [-i AFILE] [-o OUTPUT] [-x ORF]
+      
+        usage: rgi_jsontab [-h] [-i AFILE] [-o OUTPUT] [-v VERBOSE]
 
-Convert RGI JSON file to Tab-delimited file
+        Convert RGI JSON file to Tab-delimited file
 
-optional arguments:
-  -h, --help            show this help message and exit
-  -i AFILE, --afile AFILE
-                        must be a json file generated from RGI in JSON or gzip
-                        format e.g out.json, out.json.gz
-  -o OUTPUT, --out_file OUTPUT
-                        Output JSON file (default=dataSummary)
-  -x ORF, --orf ORF     choose between prodigal and MetaGeneMark orf finder.
-                        Options are 0 or 1 (default = 0 for using prodigal)
+        optional arguments:
+          -h, --help            show this help message and exit
+          -i AFILE, --afile AFILE
+                                must be a json file generated from RGI in JSON or gzip
+                                format e.g out.json, out.json.gz
+          -o OUTPUT, --out_file OUTPUT
+                                Output Tab-delimited file (default=dataSummary)
+          -v VERBOSE, --verbose VERBOSE
+                                include help menu. Options are OFF or ON (default =
+                                OFF for no help)
 
     ]]></help>
     <citations>
diff -r 679b084023ad -r 259d81207224 rgi_load.xml
--- a/rgi_load.xml	Fri Oct 14 14:28:52 2016 -0400
+++ b/rgi_load.xml	Fri Mar 17 15:34:53 2017 -0400
@@ -1,19 +1,18 @@
-<tool id="rgi_load" name="RGI: Loader" version="3.1.1">
+<tool id="rgi_load" name="Resistance Gene Identifier (RGI) - Loads new CARD data into RGI tool" version="3.1.2">
     <description>This tool loads new CARD data into RGI tool</description>
     <requirements>
-      <requirement type="package">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        rgi_load -i $input1
+        rgi_load -i "$input1"
     ]]></command>
     <inputs>
+        <param type="data" name="card" format="json" />
         <param type="data" name="input1" format="json" />
     </inputs>
     <outputs>
-        <data format="txt" name="report" label="RGI: Load Report"/>
     </outputs>
     <tests>
         <test>
@@ -21,14 +20,15 @@
         </test>
     </tests>
     <help><![CDATA[
-        usage: rgi_load [-h] [-i AFILE]
 
-Load card database json file
+            usage: rgi_load [-h] [-i AFILE]
+
+            Load card database json file
 
-optional arguments:
-  -h, --help            show this help message and exit
-  -i AFILE, --afile AFILE
-                        must be a card database json file
+            optional arguments:
+              -h, --help            show this help message and exit
+              -i AFILE, --afile AFILE
+                                    must be a card database json file
 
     ]]></help>
     <citations>
diff -r 679b084023ad -r 259d81207224 tools/shed.xml
--- a/tools/shed.xml	Fri Oct 14 14:28:52 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<?xml version="1.0"?>
-<tool_sheds>
-    <tool_shed name="Galaxy Main Tool Shed" url="http://toolshed.g2.bx.psu.edu/"/>
-    <tool_shed name="Galaxy Main Tool Shed" url="http://testtoolshed.g2.bx.psu.edu/"/>
-</tool_sheds>