diff krocus.xml @ 2:3e434415a387 draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty

--- a/krocus.xml	Thu Feb 07 12:19:52 2019 -0500
+++ b/krocus.xml	Fri Nov 15 13:47:02 2019 +0000
@@ -8,8 +8,8 @@
     <command detect_errors="exit_code"><![CDATA[
         krocus 
         --output_file detected_mlst.tsv
-        #if str($opt_args.filtered_reads_file) != ""
-            --filtered_reads_file $opt_args.filtered_reads_file
+        #if $opt_args.filtered_reads
+            --filtered_reads_file filtered_reads.fq
         #end if
         --max_gap $opt_args.max_gap
         --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
@@ -19,19 +19,12 @@
         --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
         --max_kmers $opt_args.max_kmers
         --print_interval $opt_args.print_interval
-        --kmer $opt_args.kmer
-        
-        #if $opt_args.divisible_by_3
-            --divisible_by_3
-        #end if
-        
-        #if $opt_args.verbose
-            --verbose
-        #end if
-
+        --kmer $opt_args.kmer        
+        $opt_args.divisible_by_3
+        $opt_args.verbose
         '$krocus_mlst_databases.fields.path' '$fastq'
-    ]]></command>
-    
+    ]]>
+    </command>
     <inputs>
         <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
         <param label="Select a database" name="krocus_mlst_databases" type="select">
@@ -40,40 +33,55 @@
             </options>
         </param>
         <section name="opt_args" title="Optional Arguments">
-        <param argument="--filtered_reads_file" type="text" value="" optional="True" label="Filename to save matching reads to" help="Default: None" />
-        <param argument="--max_gap" type="integer" value="4" label="Maximum gap for blocks to be contigous, measured in
+            <param name="filtered_reads" type="boolean" truevalue="" falsevalue="" checked="false" label="Save filtered reads ?"/>
+            <param argument="--max_gap" type="integer" min="1" value="4" label="Maximum gap for blocks to be contigous, measured in
                         multiples of the k-mer size" help="Default:4" />
-        <param argument="--margin" type="integer" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
-        <param argument="--min_block_size" type="integer" value="150" label="Minimum block size in bases" help="Default:150" />
-        <param argument="--min_fasta_hits" type="integer" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
-        <param argument="--min_kmers_for_onex_pass" type="integer" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
-        <param argument="--max_kmers" type="integer" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
-        <param argument="--print_interval" type="integer" value="10" label="Print ST every this number of reads" help="(Default:500)" />
-        <param argument="--kmer" type="integer" value="10" label="k-mer size" help="(Default:11)" />
-        <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
-        <param argument="--target_st" type="integer" value="" optional="True" label="For performance testing print time to find given ST" help="(Default:None)" />
-        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
+            <param argument="--margin" type="integer" min="1" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
+            <param argument="--min_block_size" type="integer" min="1" value="150" label="Minimum block size in bases" help="Default:150" />
+            <param argument="--min_fasta_hits" type="integer" min="1" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
+            <param argument="--min_kmers_for_onex_pass" type="integer" min="2" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
+            <param argument="--max_kmers" type="integer" min="1" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
+            <param argument="--print_interval" type="integer" min="1" value="10" label="Print ST every this number of reads" help="(Default:500)" />
+            <param argument="--kmer" type="integer" min="2" value="10" label="k-mer size" help="(Default:11)" />
+            <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
+            <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
         </section>
     </inputs>
 
     <outputs>
         <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
+        <data name="filtered_reads" format="fastq" label="${tool.name} on ${on_string}: Filtered reads" from_work_dir="filtered_reads.fq">
+            <filter>opt_args['filtered_reads'] is True</filter>
+        </data>
     </outputs>
 
     <tests>
-        <test>
-        <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
-        <param name="krocus_mlst_databases" value="mlst_db"/>
-        <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="contains" />
+        <test expect_num_outputs="1">
+            <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
+            <param name="krocus_mlst_databases" value="mlst_db"/>
+            <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="sim_size" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
+            <param name="filtered_reads" value="True" />
+            <param name="krocus_mlst_databases" value="mlst_db"/>
+            <output name="filtered_reads" ftype="fastq" file="filtered_reads.fq" compare="sim_size" />
         </test>
     </tests>
 
     <help><![CDATA[
-    usage: krocus [options] allele_directory input.fastq
+    Multi-locus sequence typing (MLST) from uncorrected long reads
 
-    multi-locus sequence typing (MLST) from uncorrected long reads
+    Krocus can predict a sequence type directly from uncorrected long reads, and
+    which was designed to consume read data as it is produced, providing results
+    in minutes. It is the only tool which can do this from uncorrected long
+    reads. We tested Krocus on over 600 samples sequenced with using long read
+    sequencing technologies from PacBio and Oxford Nanopore. It provides
+    sequence types on average within 90 seconds, with a sensitivity of 94% and
+    specificity of 97%, directly from uncorrected raw sequence reads.
     
     Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
-    ]]></help>
- <expand macro="citations" />
+    ]]>
+    </help>
+    <expand macro="citations" />
 </tool>