diff macros.xml @ 0:dd5398cf0eeb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 20 03:13:51 2017 -0400
@@ -0,0 +1,42 @@
+<macros>
+    <token name="@discosnp_single_reads@"><![CDATA[
+        #for $input in $input_type_options.list_reads
+            #set $filename = str($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) + "." + $paired.forward.ext
+            ln -sf '${paired.forward}' '${filenameFWD}' &&
+
+            #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext
+            ln -sf '${paired.reverse}' '${filenameREV}' &&
+
+            echo '${filenameFWD}' > "paired_${i}.lst" &&
+            echo '${filenameREV}' >> "paired_${i}.lst" &&
+            echo "paired_${i}.lst" >> input.lst &&
+
+        #end for
+    ]]></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>
+    <xml name="citations">
+        <citations>
+            <yield/>
+            <citation type="doi">10.1186/s13742-015-0105-2</citation>
+        </citations>
+    </xml>
+</macros>