# HG changeset patch
# User rliterman
# Date 1734634924 18000
# Node ID b87f07ac9edc952ec0185566ad555b9ad8bbaac6
# Parent  0552b9528fc4fca1e352ea51ef73f8785407ace3
"planemo upload"

diff -r 0552b9528fc4 -r b87f07ac9edc csp2_snp.xml
--- a/csp2_snp.xml	Thu Dec 19 13:20:18 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 14:02:04 2024 -0500
@@ -8,85 +8,63 @@
         <command detect_errors="aggressive"><![CDATA[
 mkdir ./queries ./references;
 
-#set query_fasta_input=""
-#set ref_fasta_input=""
-#set query_reads_forward=""
-#set query_reads_reverse=""
-#set ref_reads_forward=""
-#set ref_reads_reverse=""
-
-export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select"
-export QUERY_READS_SELECT="$query_reads.query_reads_select"
-export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
-export REF_READS_SELECT="$ref_reads.ref_reads_select"
-
-echo "Query Fasta: \$QUERY_FASTA_SELECT";
-echo "Ref Fasta: \$REF_FASTA_SELECT";
-
-echo "Query Reads: \$QUERY_READS_SELECT";
-echo "Ref Reads: \$REF_READS_SELECT";
-
-if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
-    #set query_fasta_input=$query_fasta.coll.elements
-elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
-    #set query_fasta_input=$query_fasta.list
-fi;
-
-if [[ "\$REF_FASTA_SELECT" == 'collection' ]]; then
-    #set ref_fasta_input=$ref_fasta.coll.elements
-elif [[ "\$REF_FASTA_SELECT" == 'history' ]]; then
-    #set ref_fasta_input=$ref_fasta.list
-fi;
-
-if [[ "\$QUERY_READS_SELECT" == 'collection' ]]; then
-    #set query_reads_forward=$query_reads.coll.forward
-    #set query_reads_reverse=$query_reads.coll.reverse
-elif [[ "\$QUERY_READS_SELECT" == 'history' ]]; then
-    #set query_reads_forward=$query_reads.list
-fi;
-
-if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
-    #set ref_reads_forward=$ref_reads.coll.forward
-    #set ref_reads_reverse=$ref_reads.coll.reverse
-elif [[ "\$REF_READS_SELECT" == 'history' ]]; then
-    #set ref_reads_forward=$ref_reads.list
-fi;
-
-if [[ "\$QUERY_FASTA_SELECT" == 'none' ]]; then
+#if (str($query_fasta.query_fasta_select) == "none"):
         export QUERY_FASTA_ARG="";
-else
-        #for query in $query_fasta_input:
-                ln -sf ${query} ./queries/${query.element_identifier};
+#elif (str($query_fasta.query_fasta_select) == "collection"):
+        #for _, $query_assembly in enumerate($query_fasta.coll):
+                ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
         #end for
         export QUERY_FASTA_ARG="--fasta ./queries";
-fi;
+#else
+        #for _, $query_assembly in enumerate($query_fasta.list):
+                ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
+        #end for
+        export QUERY_FASTA_ARG="--fasta ./queries";
+#end if
 
-if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
+#if (str($ref_fasta.ref_fasta_select) == "none"):
         export REF_FASTA_ARG="";
+#elif (str($ref_fasta.ref_fasta_select) == "collection"):
+        #for _, $ref_assembly in enumerate($ref_fasta.coll):
+                ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
+        #end for
+        export REF_FASTA_ARG="--fasta ./queries";
 else
-        #for ref in $ref_fasta_input:
-                ln -sf ${ref} ./references/${ref.element_identifier};
+        #for _, $ref_assembly in enumerate($ref_fasta.list):
+                ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
         #end for
         export REF_FASTA_ARG="--fasta ./references";
-fi;
+#end if
 
-if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
+#if (str($query_reads.query_reads_select) == "none"):
         export QUERY_READS_ARG="";
-else
-        #for query in $query_reads_forward $query_reads_reverse:
-                ln -sf ${query} ./queries/${query.element_identifier};
+#elif (str($query_reads.query_reads_select) == "collection"):
+        #for _, $pair in enumerate($query_reads.coll):
+                ln -sf '$pair.forward' ./queries/${pair.forward.element_identifier};
+                ln -sf '$pair.reverse' ./queries/${pair.reverse.element_identifier};
         #end for
         export QUERY_READS_ARG="--reads ./queries";
-fi;
+else
+        #for _, $read_file in enumerate($query_reads.list):
+                ln -sf ${read_file} ./queries/${read_file.element_identifier};
+        #end for
+        export QUERY_FASTA_ARG="--reads ./queries";
+#end if
 
-if [[ "\$REF_READS_SELECT" == "none" ]]; then
-        export QUERY_READS_ARG="";
+#if (str($ref_reads.ref_reads_select) == "none"):
+        export REF_READS_ARG="";
+#elif (str($ref_reads.ref_reads_select) == "collection"):
+        #for _, $pair in enumerate($ref_reads.coll):
+                ln -sf '$pair.forward' ./references/${pair.forward.element_identifier};
+                ln -sf '$pair.reverse' ./references/${pair.reverse.element_identifier};
+        #end for
+        export REF_READS_ARG="--ref_reads ./references";
 else
-        #for ref in $ref_reads_forward $ref_reads_reverse:
-                ln -sf ${ref} ./references/${ref.element_identifier};
+        #for _, $read_file in enumerate($ref_reads.list):
+                ln -sf ${read_file} ./references/${read_file.element_identifier};
         #end for
-        export QUERY_READS_ARG="--reads ./queries";
-fi;
+        export REF_FASTA_ARG="--ref_reads ./references";
+#end if
 
 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
         export TRIM_ARG="--trim_name $trim_name";
@@ -148,7 +126,7 @@
                 <when value="none">
                 </when>
                 <when value="collection">
-                        <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+                        <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
                 </when>
                 <when value="history">
                         <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
@@ -164,7 +142,7 @@
                 <when value="none">
                 </when>
                 <when value="collection">
-                        <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+                        <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
                 </when>
                 <when value="history">
                         <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
@@ -178,13 +156,13 @@
                 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
                 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" />
                 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
-                <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
-                <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
-                <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
+                <param name="readext" type="text" value="fq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
+                <param name="forward" type="text" value="_1.fq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
+                <param name="reverse" type="text" value="_2.fq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
                 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
                 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
                 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
-                <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
+                <param name="n_ref" type="integer" value="2" label="Number of reference genomes to select" optional="true" />
 
         </inputs>
         <outputs>