bug fixes

arpcard · May 9, 2017 · fe7b246 · fe7b246
1 parent 1460768
commit fe7b246
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Showing 2 changed files with 27 additions and 28 deletions.
diff --git a/rgi.xml b/rgi.xml
@@ -9,7 +9,6 @@
         <requirement type="package" version="2.6.0">blast</requirement>
         <requirement type="package" version="0.8.36">diamond</requirement>
         <requirement type="package" version="1.2.8">zlib</requirement>
-
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -18,108 +17,110 @@
         rgi --input_sequence $input_sequence --input_type $input_type --num_threads "\${GALAXY_SLOTS:-32}" --clean_databases NO --verbose $verbose --alignment_tool $alignment_tool --loose_criteria $loose_criteria --clean $clean --db "${__tool_data_path__}/rgi_databases/$rgi_databases"
     ]]></command>
     <inputs>
-
-        <param type="data" name="input_sequence" format="fastq,fasta" label="Input Sequence" />
-
+        <param type="data" name="input_sequence" format="fastq,fasta" label="Input Sequence"/>
         <param type="select" name="input_type"  label="Input Type" multiple="false">
             <option value="contig" selected="true">CONTIG (Nucluotides Sequence)</option>
             <option value="protein">PROTEIN (Protein Sequence)</option>
             <option value="read">READ (Metagenomics Sequence / FastQ)</option>
         </param>
-
         <param type="select" name="alignment_tool"  label="Alignment Tool">
             <option value="blast" selected="true">BLAST</option>
             <option value="diamond">DIAMOND</option>
         </param>
-
         <param type="select" name="verbose"  label="Log progress to file (VERBOSE)" multiple="false">
             <option value="off" selected="true">OFF</option>
             <option value="on">ON</option>
         </param>
-
         <param type="select" name="clean"  label="Remove temporary files (CLEAN)" multiple="false">
             <option value="yes" selected="true">YES</option>
             <option value="no">NO</option>
         </param>
-
         <param type="select" name="loose_criteria" label="Include loose hits (CRITERIA)" multiple="false">
           <option value="yes">YES</option>
           <option value="no" selected="true">NO</option>
         </param>
-
         <param label="Select a RGI database" name="rgi_databases" type="select">
             <options from_data_table="rgi_databases">
                 <validator message="No databases are available built-in" type="no_options" />
             </options>
         </param>
-
     </inputs>
-
     <outputs>
         <data format="json" name="Report" from_work_dir="Report.json" label="${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>
-    </outputs>  
-
+    </outputs>
     <tests>
         <test>
             <param name="inType" value="protein"/>
             <param name="inputSeq" value="inputSeq.fasta"/>
             <output name="Report" file="Report.json"/>
         </test>
     </tests>
-    <help><![CDATA[
-
+    <help>
+      <![CDATA[
         usage: rgi [-h] [-t INTYPE] [-i INPUTSEQ] [-n THREADS] [-k NUM_SEQUENCES]
-                      [-o OUTPUT] [-e CRITERIA] [-c CLEAN] [-cd CLEAN_DATABASES]
-                      [-d DATA] [-l VERBOSE] [-a ALIGNER] [-r DATABASE] [-sv] [-dv]
+                   [-o OUTPUT] [-e CRITERIA] [-c CLEAN] [-cd CLEAN_DATABASES]
+                   [-d DATA] [-l VERBOSE] [-a ALIGNER] [-r DATABASE] [-sv] [-dv]
 
         Resistance Gene Identifier - Version 3.2.0
 
         optional arguments:
           -h, --help            show this help message and exit
           -t INTYPE, --input_type INTYPE
-                                must be one of contig, protein and read (default:
-                                contig)
+                                must be one of contig, protein and 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)
+
           -k NUM_SEQUENCES, --max_target_seqs NUM_SEQUENCES
                                 maximum number of target sequences to report
                                 alignments for (default=1)
+
           -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)
-          -cd CLEAN_DATABASES, --clean_databases CLEAN_DATABASES
+                                after run. Options are NO or YES (default=YES for remove)
+
+          --clean_databases CLEAN_DATABASES
                                 This removes blast databases before rgi 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>
+          -dv, --data_version   
+                                Prints data version number
+    ]]>
+    </help>
     <citations>
         <citation type="bibtex">
 @misc{renameTODO,

diff --git a/rgi_jsontab.xml b/rgi_jsontab.xml
@@ -7,15 +7,13 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        rgi_jsontab -i "$input1" -o "$output1"
+        rgi_jsontab -i "$input1"
     ]]></command>
     <inputs>
-        <param type="data" name="Report" format="json" />
         <param type="data" name="input1" format="json" />
     </inputs>
     <outputs>
-        <data name="dataSummary" format="txt" />
-        <data name="output1" format="txt" />
+        <data format="tabular" name="dataSummary" from_work_dir="dataSummary.txt" label="${tool.name} on ${on_string}: (TXT)" />
     </outputs>
     <tests>
         <test>