diff circlator.xml @ 1:34810a7283ba draft

planemo upload

--- a/circlator.xml	Fri May 17 10:52:31 2019 -0400
+++ b/circlator.xml	Mon May 20 05:17:10 2019 -0400
@@ -3,7 +3,9 @@
      This task runs the complete Circlator pipeline. It runs the tasks: progcheck, mapreads, bam2reads, assemble, merge, clean, fixstart.
   </description>
   <requirements>
-    <requirement type="package" version="1.5.5">circlator</requirement>
+    <requirement type="package" version="1.5.5=py_2">circlator</requirement>
+    <requirement type="package" version="3.23">mummer</requirement>
+    <requirement type="package" version="1.6">canu</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     circlator all 
@@ -36,56 +38,59 @@
     #end if
     $file_contigs $file_reads outdir
     ]]></command>
+  <environment_variables>
+    <environment_variable name="LC_ALL">C</environment_variable>
+  </environment_variables>
   <inputs>
     <param type="data" name="file_reads" label="Reads to be mapped to contig, in any format BWA MEM accepts" format="fastqsanger,fastqsanger.gz,fasta, fasta.gz" />
     <param type="data" name="file_contigs" label="Assembly (contigs)" format="fasta" />
 
     <section name="assembly" title="Assembly">
-    <conditional name="canu_or_spades">
-      <param name="assembler" type="select" label="Assembler to use for reassemblies" >
-        <option value="spades" selected="true">SPAdes</option>
-        <option value="canu">Canu</option>
-      </param>
-      <when value="canu">
-        <param name="datatype" type="select" label="one of the 4 types of data analysed" >
-          <option value="pacbio-corrected" selected="true">pacbio corrected</option>
-          <option value="pacbio-raw">pacbio raw</option>
-          <option value="nanopore-corrected">nanopore corrected</option>
-          <option value="nanopore-raw">nanopore raw</option>
+      <conditional name="canu_or_spades">
+        <param name="assembler" type="select" label="Assembler to use for reassemblies" >
+          <option value="spades" selected="true">SPAdes</option>
+          <option value="canu">Canu</option>
         </param>
-      </when>
-      <when value="spades">
-        <param name="not_careful" argument="--assemble_not_careful" type="boolean" truevalue="--assemble_not_careful" falsevalue="" checked="false" 
-          label="Do not use the --careful option with SPAdes" help="note that this circlator option is to NOT use an option from SPAdes; if unsure, leave it unchekced" />
-        <param name="not_only_assembler" argument="--assemble_not_only_assembler" truevalue="--assemble_not_only_assembler" falsevalue=""
-          type="boolean" checked="false" label="Do not use the --assemble-only option with SPAdes. Important: with this option, the input reads must 
-          be in FASTQ format, otherwise SPAdes will crash because it needs quality scores to correct the reads." 
-          help="note that this circlator option is to NOT use an option from SPAdes; if unsure, leave it unchecked"/>
-      </when>
-    </conditional>
-    <param name="split_all_reads" argument="--split_all_reads" type="boolean" truevalue="--split_all_reads" falsevalue="" checked="false" 
-      label="By default, reads mapped to shorter contigs are left unchanged. This option splits them into two, broken at the middle of the 
-      contig to try to force circularization. May help if the assembler does not detect circular contigs (eg canu)" />
-    <param name="assemble_spades_use_first" argument="--assemble_spades_use_first" truevalue="--assemble_spades_use_first" falsevalue=""
-      checked="false" type="boolean" label="Use the first successful SPAdes assembly. Default is to try all kmers and use the assembly with 
-      the largest N50" />
-  
-  </section>
-  <section name="mapreads" title="mapreads options">
-    <param name="bwa_opts" type="text" label="text with BWA options (exactly as used by BWA MEM)"/>
-  </section>
+        <when value="canu">
+          <param name="datatype" type="select" label="one of the 4 types of data analysed" >
+            <option value="pacbio-corrected" selected="true">pacbio corrected</option>
+            <option value="pacbio-raw">pacbio raw</option>
+            <option value="nanopore-corrected">nanopore corrected</option>
+            <option value="nanopore-raw">nanopore raw</option>
+          </param>
+        </when>
+        <when value="spades">
+          <param name="not_careful" argument="--assemble_not_careful" type="boolean" truevalue="--assemble_not_careful" falsevalue="" checked="false" 
+            label="Do not use the --careful option with SPAdes" help="note that this circlator option is to NOT use an option from SPAdes; if unsure, leave it unchekced" />
+          <param name="not_only_assembler" argument="--assemble_not_only_assembler" truevalue="--assemble_not_only_assembler" falsevalue=""
+            type="boolean" checked="false" label="Do not use the --assemble-only option with SPAdes. Important: with this option, the input reads must 
+            be in FASTQ format, otherwise SPAdes will crash because it needs quality scores to correct the reads." 
+            help="note that this circlator option is to NOT use an option from SPAdes; if unsure, leave it unchecked"/>
+        </when>
+      </conditional>
+      <param name="split_all_reads" argument="--split_all_reads" type="boolean" truevalue="--split_all_reads" falsevalue="" checked="false" 
+        label="By default, reads mapped to shorter contigs are left unchanged. This option splits them into two, broken at the middle of the 
+        contig to try to force circularization. May help if the assembler does not detect circular contigs (eg canu)" />
+      <param name="assemble_spades_use_first" argument="--assemble_spades_use_first" truevalue="--assemble_spades_use_first" falsevalue=""
+        checked="false" type="boolean" label="Use the first successful SPAdes assembly. Default is to try all kmers and use the assembly with 
+        the largest N50" />
 
-  <section name="bam2read" title="bam2reads options">
-    <param name="b2r_discard" argument="--b2r_discard_unmapped" truevalue="--b2r_discard_unmapped" falsevalue="" checked="false" type="boolean"
-      label="Check this to not keep unmapped reads" />
-    <param name="b2r_length_cutoff" type="integer" label="All reads mapped to contigs shorter than this will be kept (default=100000)" optional="true"/>
-    <param name="b2r_min_read_length" type="integer" label="Minimum length of read to output (defaul=250)" optional="true"/>
-  </section>
+    </section>
+    <section name="mapreads" title="mapreads options">
+      <param name="bwa_opts" type="text" label="text with BWA options (exactly as used by BWA MEM)"/>
+    </section>
 
-  <section name="fix" title="fixstart options">
-    <param name="fixstart_mincluster" type="integer" label="The -c|mincluster option of promer. Overrides promer's default value" optional="true"/>
-    <param name="fixstart_min_id" type="float" label="Minimum percent identity of promer match between contigs and gene(s) to use as start point (dafault=70)" optional="true"/>
-  </section>
+    <section name="bam2read" title="bam2reads options">
+      <param name="b2r_discard" argument="--b2r_discard_unmapped" truevalue="--b2r_discard_unmapped" falsevalue="" checked="false" type="boolean"
+        label="Check this to not keep unmapped reads" />
+      <param name="b2r_length_cutoff" type="integer" label="All reads mapped to contigs shorter than this will be kept (default=100000)" optional="true"/>
+      <param name="b2r_min_read_length" type="integer" label="Minimum length of read to output (defaul=250)" optional="true"/>
+    </section>
+
+    <section name="fix" title="fixstart options">
+      <param name="fixstart_mincluster" type="integer" label="The -c|mincluster option of promer. Overrides promer's default value" optional="true"/>
+      <param name="fixstart_min_id" type="float" label="Minimum percent identity of promer match between contigs and gene(s) to use as start point (dafault=70)" optional="true"/>
+    </section>
 
   </inputs>
   <outputs>
@@ -109,14 +114,12 @@
 
     Any contigs that were identified as circular then have their start position changed.
 
-    Currently it does not use CANU (only SPAdes), it does not download the uniprot database and it does not run the minimus2 pipeline.
+    Currently it does not download the uniprot database and it does not run the minimus2 pipeline. Even when running canu it may give warning messages about the SPAdes version, 
+    you can safely ignore those.
     ]]></help>
   <citations>
     <citation type="bibtex">
       @misc{github,
-      author = {LastTODO, FirstTODO},
-      year = {TODO},
-      title = {},
       publisher = {GitHub},
       journal = {GitHub repository},
       url = {https://github.com/sanger-pathogens/circlator/},