diff macros.xml @ 1:13c8e1ce0a15 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6

--- a/macros.xml	Fri Oct 20 03:13:51 2017 -0400
+++ b/macros.xml	Fri Nov 24 12:47:46 2017 -0500
@@ -1,18 +1,27 @@
 <macros>
+    <xml name="discosnp_requirements">
+        <requirements>
+            <requirement type="package" version="2.3.0">discosnp</requirement>
+        </requirements>
+    </xml>
+
+    <token name="@DISCOSNP_VERSION@">2.3.0</token>
+
     <token name="@discosnp_single_reads@"><![CDATA[
         #for $input in $input_type_options.list_reads
-            #set $filename = str($input) + "." + $input.ext
+            #set $filename = os.path.basename(str($input)) + "." + $input.ext
             ln -sf '${input}' '${filename}' &&
             echo '${filename}' >> input.lst &&
         #end for
     ]]></token>
+
     <token name="@discosnp_paired_reads@"><![CDATA[
         #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
 
-            #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext
+            #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
             ln -sf '${paired.forward}' '${filenameFWD}' &&
 
-            #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext
+            #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
             ln -sf '${paired.reverse}' '${filenameREV}' &&
 
             echo '${filenameFWD}' > "paired_${i}.lst" &&
@@ -21,22 +30,121 @@
 
         #end for
     ]]></token>
+
+    <xml name="discosnp_inputs">
+        <conditional name="input_type_options">
+            <param name="input_type" type="select" label="Input options">
+                <option value="single">Single end reads</option>
+                <option value="paired">Paired end reads</option>
+                <option value="mix">Both single and paired reads</option>
+            </param>
+            <when value="single">
+                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
+            </when>
+            <when value="paired">
+                <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
+            </when>
+            <when value="mix">
+                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
+                <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="discosnp_options">
+        <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/>
+        <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/>
+        <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
+        <param argument="-k" type="integer" label="Size of kmers" value="31" />
+
+        <conditional name="coverage_options_type" >
+            <param name="coverage_options" type="select" label="Coverage option">
+                <option value="auto"></option>
+                <option value="custom"></option>
+            </param>
+            <when value="auto" />
+            <when value="custom">
+                <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
+            </when>
+        </conditional>
+
+        <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
+        <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
+
+    </xml>
+
+    <token name="@discosnp_inputs@"><![CDATA[
+        -r input.lst
+        -b ${b}
+        -D ${D}
+        -P ${P}
+        ${low_complexity}
+        -k ${k}
+
+        #if str($coverage_options_type.coverage_options) == 'auto'
+            -c auto
+        #else
+            -c '${coverage_options_type.c}'
+        #end if
+        -C ${C}
+        -d ${d}
+    ]]></token>
+
     <token name="@lordec_inputs@"><![CDATA[
         -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
         -i '${program_type_choice.i}'
         -k ${program_type_choice.k}
         -s ${program_type_choice.s}
     ]]></token>
+
     <xml name="lordec_inputs">
         <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
         <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
         <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
         <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
     </xml>
+
+    <token name="@discosnp_help@"><![CDATA[
+-------
+
+.. class:: warningmark
+
+**Input parameters**
+
+-Sequences files in fasta or fastq each allele will be counted in each file individually
+
+-Use collections: data list and/or data list paired
+
+-Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
+
+-------
+
+.. class:: warningmark
+
+**Ouput parameters**
+
+-VCF file with coordinates on the higher branch sequences or on a reference genome if provided
+
+-Fasta file with sequence extensions around the SNP.
+
+
+-------
+
+**Web site**
+
+https://colibread.inria.fr/software/discosnp/
+
+    ]]></token>
+
     <xml name="citations">
         <citations>
             <yield/>
             <citation type="doi">10.1186/s13742-015-0105-2</citation>
         </citations>
     </xml>
+
+    <xml name="discosnp_citation">
+        <citation type="doi">10.1101/209965</citation>
+    </xml>
+
 </macros>