# HG changeset patch
# User iuc
# Date 1544553287 18000
# Node ID fbe9ee43bc13f1395df3f30ce866bc0fcf5e8cf7
# Parent  2682640145c89e333198b35c6912d23b23ee73b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9

diff -r 2682640145c8 -r fbe9ee43bc13 spades.xml
--- a/spades.xml	Tue Oct 30 20:26:40 2018 -0400
+++ b/spades.xml	Tue Dec 11 13:34:47 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="spades" name="SPAdes" version="@TOOL_VERSION@">
+<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">
     <description>genome assembler for regular and single-cell projects</description>
     <macros>
         <import>macros.xml</import>
@@ -20,7 +20,7 @@
     <command>
     <![CDATA[
     ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
-    
+
     if [[ -n \$GALAXY_MEMORY_MB ]]; then
         GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
     fi &&
@@ -49,17 +49,17 @@
         --$prefix$i-$library.orientation
         #for $file in $library.files
             #if $file.file_type.type == "separate"
-                --$prefix$i-1 $file.file_type.fwd_reads.extension:$file.file_type.fwd_reads
-                --$prefix$i-2 $file.file_type.fwd_reads.extension:$file.file_type.rev_reads
+                --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads
+                --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads
             #elif $file.file_type.type == "interleaved"
-                --$prefix$i-12 $file.file_type.interleaved_reads.extension:$file.file_type.interleaved_reads
+                --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads
             #elif $file.file_type.type == "merged"
-                --$prefix$i-m $file.file_type.merged_reads.extension:$file.file_type.merged_reads
+                --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads
             #elif $file.file_type.type == "unpaired"
-                --$prefix$i-s $file.file_type.unpaired_reads.extension:$file.file_type.unpaired_reads
+                --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads
             #elif $file.file_type.type == "paired-collection"
-                --$prefix$i-1 $file.file_type.fastq_collection.forward.extension:$file.file_type.fastq_collection.forward
-                --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension:$file.file_type.fastq_collection.reverse
+                --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward
+                --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse
             #end if
         #end for
     #end for
@@ -75,24 +75,24 @@
     #end for
     #for $read in $sanger_reads:
         #if $read:
-            --sanger $read.extension:$read
+            --sanger $read.extension.replace('fastqsanger', 'fastq'):$read
         #end if
     #end for
     #for $contig in $trusted_contigs:
         #if $contig:
-            --trusted-contigs $contig.extension:$contig
+            --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
         #end if
     #end for
     #for $contig in $untrusted_contigs:
         #if $contig:
-            --untrusted-contigs $contig.extension:$contig
+            --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
         #end if
     #end for
     && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
     && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
     ]]>
     </command>
-    
+
     <configfiles>
         <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
 import sys,re
@@ -106,14 +106,14 @@
 ]]>
          </configfile>
     </configfiles>
-    
+
     <inputs>
         <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
             <option value="false">No</option>
             <option value="true">Yes</option>
         </param>
         <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
-        <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
+        <param argument="--careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
         <conditional name="kmer_choice">
             <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
             <when value="false">
@@ -219,7 +219,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 1 - basic test with k=33 fasta input -->
+        <test> <!-- Test 2 - basic test with k=33 fasta input -->
             <param name="sc" value="false" />
             <param name="onlyassembler" value="true"/>
             <param name="careful" value="false" />
@@ -234,7 +234,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 1 - basic test with k=33 and gzipped input -->
+        <test> <!-- Test 3 - basic test with k=33 and gzipped input -->
             <param name="sc" value="false" />
             <param name="careful" value="false" />
             <param name="kmers" value="33" />
@@ -248,7 +248,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 2 - auto k -->
+        <test> <!-- Test 4 - auto k -->
             <param name="sc" value="false" />
             <param name="careful" value="false" />
             <param name="auto_kmer_choice" value="true" />
@@ -257,7 +257,7 @@
             <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
             <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
         </test>
-        <test> <!-- Test 3 - k=77 -->
+        <test> <!-- Test 5 - k=77 -->
             <param name="sc" value="false" />
             <param name="careful" value="false" />
             <param name="kmers" value="77" />
@@ -266,7 +266,7 @@
             <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
             <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
         </test>
-        <test> <!-- Test 4 - test for extra graph outputs -->
+        <test> <!-- Test 6 - test for extra graph outputs -->
             <param name="sc" value="false" />
             <param name="careful" value="false" />
             <param name="kmers" value="33" />
@@ -292,6 +292,34 @@
                 </assert_contents>
             </output>
         </test>
+        <test> <!-- Test 7 - basic test with k=33 and fastsanger input -->
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="kmers" value="33" />
+            <param name="lib_type" value="paired_end" />
+            <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" />
+            <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" />
+            <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
+            <output name="out_contig_stats">
+                <assert_contents>
+                    <has_text_matching expression="NODE_1\t1000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input -->
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="kmers" value="33" />
+            <param name="lib_type" value="paired_end" />
+            <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
+            <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
+            <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
+            <output name="out_contig_stats">
+                <assert_contents>
+                    <has_text_matching expression="NODE_1\t1000"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[