diff abyss-pe.xml @ 7:841084c5fc46 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"

--- a/abyss-pe.xml	Mon Sep 13 16:58:30 2021 +0000
+++ b/abyss-pe.xml	Wed Oct 20 12:50:40 2021 +0000
@@ -4,7 +4,7 @@
         <xref type="bio.tools">abyss</xref>
     </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">2.3.1</token>
+        <token name="@TOOL_VERSION@">2.3.2</token>
         <xml name="reads_conditional">
             <conditional name="reads">
                 <param name="reads_selector" type="select" label="Type of paired-end datasets">
@@ -37,10 +37,11 @@
         <regex match="Exception:" />
     </stdio>
     <version_command>ABYSS --version | head -n 1</version_command>
-    <command>
+    <command><![CDATA[
 abyss-pe
 name=abyss
 j=\${GALAXY_SLOTS:-1}
+B=\${GALAXY_MEMORY_MB:-2048}M
 k=$k
 
 #if str($K)
@@ -91,11 +92,11 @@
 #if str($d)
     d=$d
 #end if
-#if str($S)
-    S=$S
+#if $S
+    S='$S'
 #end if
-#if str($N)
-    N=$N
+#if $N
+    N='$N'
 #end if
 #if $lib_repeat
     lib='
@@ -146,7 +147,7 @@
         long${i}='$v'
     #end for
 #end if
-    </command>
+    ]]></command>
 
     <inputs>
         <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
@@ -167,15 +168,19 @@
         <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
         <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
         <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
-        <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
+        <param argument="m" type="integer" value="" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="Defaults to 0 (interpreted as k - 1) if mate-pair libraries are provided or if k&lt;=50, otherwise 50" />
         <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
         <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
         <param argument="l" type="integer" value="" min="1"  optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
         <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
         <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
         <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
-        <param argument="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s" />
-        <param argument="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n" />
+        <param argument="S" type="text" value="" label="Minimum contig size required for building scaffolds (in bp)" help="It can be an interval. Defaults to 100-5000">
+            <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
+        </param>
+        <param argument="N" type="text" value="" label="Minimum number of pairs required for building scaffolds" help="It can be an interval. Defaults to 15-20">
+            <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
+        </param>
     </inputs>
 
     <outputs>
@@ -189,9 +194,7 @@
         <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
             <filter>long_seqs</filter>
         </data>
-        <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
         <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
-        <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
         <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
     </outputs>
 
@@ -208,18 +211,14 @@
             <output name="unitigs" file="abyss-unitigs1.fa" />
             <output name="contigs_outfile" file="abyss-contigs1.fa" />
             <output name="scaffolds" file="abyss-scaffolds1.fa" />
-            <output name="bubbles" file="empty_file.fasta" />
             <output name="indels" file="empty_file.fasta" />
-            <output name="coverage_histogram_outfile" file="coverage1.hist" />
             <output name="stats" file="abyss-stats1.tab" />
         </test>
         <test>
             <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
             <param name="k" value="50" />
             <output name="unitigs" file="abyss-unitigs2.fa" />
-            <output name="bubbles" file="empty_file.fasta" />
             <output name="indels" file="empty_file.fasta" />
-            <output name="coverage_histogram_outfile" file="coverage2.hist" />
             <output name="stats" file="abyss-stats2.tab" />
         </test>
         <test>
@@ -228,13 +227,11 @@
             <param name="k" value="50" />
             <output name="unitigs" file="abyss-unitigs3.fa" />
             <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
-            <output name="bubbles" file="empty_file.fasta" />
             <output name="indels" file="empty_file.fasta" />
-            <output name="coverage_histogram_outfile" file="coverage3.hist" />
             <output name="stats" file="abyss-stats3.tab" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
@@ -255,7 +252,7 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2015-2021 `Earlham Institute`_ and is released under the `MIT license`_.
 
 .. _Earlham Institute: http://www.earlham.ac.uk/
 .. _MIT license: https://opensource.org/licenses/MIT
@@ -263,8 +260,9 @@
 You can use this tool only if you agree to the license terms of: `ABySS`_.
 
 .. _ABySS: https://github.com/bcgsc/abyss
-    </help>
+    ]]></help>
     <citations>
+        <citation type="doi">doi:10.1101/gr.214346.116</citation>
         <citation type="doi">10.1101/gr.089532.108</citation>
     </citations>
 </tool>