| Previous changeset 9:24fffa4fee40 (2018-10-30) Next changeset 11:b8c00ce5dfa0 (2019-11-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 |
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modified:
spades.xml |
| b |
| diff -r 24fffa4fee40 -r b8d633fbf5f5 spades.xml --- a/spades.xml Tue Oct 30 20:27:11 2018 -0400 +++ b/spades.xml Tue Dec 11 13:36:00 2018 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="spades" name="SPAdes" version="@TOOL_VERSION@">\n+<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">\n <description>genome assembler for regular and single-cell projects</description>\n <macros>\n <import>macros.xml</import>\n@@ -20,7 +20,7 @@\n <command>\n <![CDATA[\n ## 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\n- \n+\n if [[ -n \\$GALAXY_MEMORY_MB ]]; then\n GALAXY_MEMORY_GB=\\$(( GALAXY_MEMORY_MB / 1024 ));\n fi &&\n@@ -49,17 +49,17 @@\n --$prefix$i-$library.orientation\n #for $file in $library.files\n #if $file.file_type.type == "separate"\n- --$prefix$i-1 $file.file_type.fwd_reads.extension:$file.file_type.fwd_reads\n- --$prefix$i-2 $file.file_type.fwd_reads.extension:$file.file_type.rev_reads\n+ --$prefix$i-1 $file.file_type.fwd_reads.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.fwd_reads\n+ --$prefix$i-2 $file.file_type.fwd_reads.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.rev_reads\n #elif $file.file_type.type == "interleaved"\n- --$prefix$i-12 $file.file_type.interleaved_reads.extension:$file.file_type.interleaved_reads\n+ --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.interleaved_reads\n #elif $file.file_type.type == "merged"\n- --$prefix$i-m $file.file_type.merged_reads.extension:$file.file_type.merged_reads\n+ --$prefix$i-m $file.file_type.merged_reads.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.merged_reads\n #elif $file.file_type.type == "unpaired"\n- --$prefix$i-s $file.file_type.unpaired_reads.extension:$file.file_type.unpaired_reads\n+ --$prefix$i-s $file.file_type.unpaired_reads.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.unpaired_reads\n #elif $file.file_type.type == "paired-collection"\n- --$prefix$i-1 $file.file_type.fastq_collection.forward.extension:$file.file_type.fastq_collection.forward\n- --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension:$file.file_type.fastq_collection.reverse\n+ --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.fastq_collection.forward\n+ --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace(\'fastqsanger\', \'fastq\'):$file.file_type.fastq_collection.reverse\n #end if\n #end for\n #end for\n@@ -75,24 +75,24 @@\n #end for\n #for $read in $sanger_reads:\n #if $read:\n- --sanger $read.extension:$read\n+ --sanger $read.extension.replace(\'fastqsanger\', \'fastq\'):$read\n #end if\n #end for\n #for $contig in $trusted_contigs:\n #if $contig:\n- --trusted-contigs $contig.extension:$contig\n+ --trusted-contigs $contig.extension.replace(\'fastqsanger\', \'fastq\'):$contig\n #end if\n #end for\n #for $contig in $untrusted_contigs:\n #if $contig:\n- --untrusted-contigs $contig.extension:$contig\n+ --untrusted-contigs $contig.extension.replace(\'fastqsanger\', \'fastq\'):$contig\n #end if\n #end for\n && python \'$write_tsv_script\' < contigs.fasta > \'$out_contig_stats\'\n && python \'$write_tsv_script\' < scaffolds.fasta > \'$out_scaffold_stats\'\n ]]>\n </command>\n- \n+\n <configfiles>\n <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python\n import sys,re\n@@ -106,14 +106,14 @@\n ]]>\n </configfile>\n </configfiles>\n- \n+\n <inputs>\n <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">\n '..b'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" />\n <when value="false">\n@@ -219,7 +219,7 @@\n </assert_contents>\n </output>\n </test>\n- <test> <!-- Test 1 - basic test with k=33 fasta input -->\n+ <test> <!-- Test 2 - basic test with k=33 fasta input -->\n <param name="sc" value="false" />\n <param name="onlyassembler" value="true"/>\n <param name="careful" value="false" />\n@@ -234,7 +234,7 @@\n </assert_contents>\n </output>\n </test>\n- <test> <!-- Test 1 - basic test with k=33 and gzipped input -->\n+ <test> <!-- Test 3 - basic test with k=33 and gzipped input -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="kmers" value="33" />\n@@ -248,7 +248,7 @@\n </assert_contents>\n </output>\n </test>\n- <test> <!-- Test 2 - auto k -->\n+ <test> <!-- Test 4 - auto k -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="auto_kmer_choice" value="true" />\n@@ -257,7 +257,7 @@\n <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />\n <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n </test>\n- <test> <!-- Test 3 - k=77 -->\n+ <test> <!-- Test 5 - k=77 -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="kmers" value="77" />\n@@ -266,7 +266,7 @@\n <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />\n <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n </test>\n- <test> <!-- Test 4 - test for extra graph outputs -->\n+ <test> <!-- Test 6 - test for extra graph outputs -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="kmers" value="33" />\n@@ -292,6 +292,34 @@\n </assert_contents>\n </output>\n </test>\n+ <test> <!-- Test 7 - basic test with k=33 and fastsanger input -->\n+ <param name="sc" value="false" />\n+ <param name="careful" value="false" />\n+ <param name="kmers" value="33" />\n+ <param name="lib_type" value="paired_end" />\n+ <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" />\n+ <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" />\n+ <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n+ <output name="out_contig_stats">\n+ <assert_contents>\n+ <has_text_matching expression="NODE_1\\t1000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input -->\n+ <param name="sc" value="false" />\n+ <param name="careful" value="false" />\n+ <param name="kmers" value="33" />\n+ <param name="lib_type" value="paired_end" />\n+ <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />\n+ <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />\n+ <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n+ <output name="out_contig_stats">\n+ <assert_contents>\n+ <has_text_matching expression="NODE_1\\t1000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |