diff quast.xml @ 5:81df4950d65b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa

--- a/quast.xml	Mon Feb 12 09:05:20 2018 -0500
+++ b/quast.xml	Tue Dec 04 06:49:05 2018 -0500
@@ -1,60 +1,46 @@
-<tool id="quast" name="Quast" version="4.6.3" >
+<tool id="quast" name="Quast" version="5.0.2" >
     <description>Genome assembly Quality</description>
     <requirements>
-        <requirement type="package" version="4.6.3">quast</requirement>
+        <requirement type="package" version="5.0.2">quast</requirement>
     </requirements>
-    <stdio>
-        <regex match="ERROR! exception caught!"
-            source="both"
-            level="fatal"
-            description="Something went wrong. Check the following errors : No labels..." />
-    </stdio>
-    <command>
+    <command detect_errors="exit_code">
     <![CDATA[
-        #import re
-        quast
-        --threads \${GALAXY_SLOTS:-4}
-        -o outputdir
-        #if $gene_selection == "eukaryote":
-            --eukaryote
-        #else if $gene_selection == "metagenes":
-            --meta
-        #end if
-        #if $input_ref:
-            -R '$input_ref'
-            #if $input_operon:
-                -O '$input_operon'
-            #end if
-            #if $annot:
-                -G '$annot'
-            #end if
-        #end if
-        #if $input_size:
-            --est-ref-size $input_size
-        #end if
-        --min-contig $min_contig
-        -l
-        #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.element_identifier))+'"' for $x in $input ])
+#import re
+quast
+--threads \${GALAXY_SLOTS:-4}
+-o outputdir
+#if $gene_selection == "eukaryote":
+    --eukaryote
+#else if $gene_selection == "metagenes":
+    --meta
+#end if
+$large
+#if $input_ref:
+    -R '$input_ref'
+    #if $input_operon:
+        -O '$input_operon'
+    #end if
+    #if $annot:
+        -g '$annot'
+    #end if
+#end if
+#if $input_size:
+    --est-ref-size $input_size
+#end if
+--min-contig $min_contig
+-l
+#set names = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $input ])
 
-        $names
-        --contig-thresholds $threshold_contig
-        #for $k in $input:
-            $k 
-        #end for
-        &&
-        mv outputdir/report.tsv '$quast_tsv' &&
-        ## The sed string below removes non-functional "Main menu" button from the viewer
-        sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/contig_size_viewer.html > '$contig_size_viewer' &&
-        #if $input_ref:
-            ## The sed string below removes non-functional "Main menu" button from the viewer
-            sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/alignment_viewer.html > '$alignment_viewer' &&
-        #end if
-        ## The sed string below removes non-functional link from the report page
-        sed "\:<div id='icarus-json'>:,\:</div>:d" outputdir/report.html > '$report_html' &&
-        mv outputdir/report.pdf '$report_pdf' &&
-        mv outputdir/contigs_reports/misassemblies_report.tsv '$mis_ass_tsv' &&
-        mv outputdir/contigs_reports/unaligned_report.tsv '$unalign_tsv' &&
-        mv outputdir/quast.log '$log_txt'
+'$names'
+--contig-thresholds $threshold_contig
+#for $k in $input:
+    $k 
+#end for
+&& mkdir '$report_html.files_path'
+&& cp outputdir/*.html '$report_html.files_path'
+#if str($input_ref):
+    && cp -R outputdir/icarus_viewers '$report_html.files_path'
+#end if
     ]]>
     </command>
     <inputs>
@@ -65,6 +51,7 @@
         </param>
         <param name="input_size" type="integer" label="Size of reference genome" optional="True"  argument="--est-ref-size"
             help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
+        <param argument="--large" type="boolean" truevalue="--large" falsevalue="" label="Run quast in --large mode for large genomes" help="Uses minimap2 aligner, improves transposable element handling and alignment thresholds"/>
         <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True"  argument="-R"
             help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
         <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G"
@@ -80,20 +67,16 @@
             help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/>
     </inputs>
     <outputs>
-        <data format="txt" name="log_txt" label="Quast: Log" />
-        <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies">
-            <filter>input_ref is not None</filter>
-        </data>
-        <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs">
+        <data format="txt" name="log_txt" label="Quast: Log" from_work_dir="outputdir/quast.log"/>
+        <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
             <filter>input_ref is not None</filter>
         </data>
-        <data format="html" name="contig_size_viewer" label="Quast: Contig view"/>
-        <data format="html" name="alignment_viewer" label="Quast: Alignment view">
+        <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
             <filter>input_ref is not None</filter>
         </data>
-        <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)"/>
-        <data format="html" name="report_html" label="Quast: Report (HTML)"/>
-        <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/>
+        <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)" from_work_dir="outputdir/report.tsv"/>
+        <data format="html" name="report_html" label="Quast: Report (HTML)" from_work_dir="outputdir/report.html"/>
+        <data format="pdf" name="report_pdf" label="Quast: Report (PDF)" from_work_dir="outputdir/report.pdf"/>
     </outputs>
     <tests>
         <test>
@@ -103,6 +86,7 @@
             <param name="type_file" value="contig"/>
             <param name="annot" value="genes.gff"/>
             <param name="gene_selection" value="prokaryotes"/>
+            <param name="large" value="true"/>
             <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/>
         </test>
         <test>
@@ -110,6 +94,8 @@
             <param name="input" value="contigs2.fna,contigs1.fna"/>
             <param name="type_file" value="contig"/>
             <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/>
+            <output name="report_html" file="test2_report.html" lines_diff="50"/>
+            <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/>
         </test>
     </tests>
     <help>