| Previous changeset 17:66f992977578 (2017-11-14) Next changeset 19:97d1923c8c4b (2018-01-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9 |
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modified:
bowtie2_wrapper.xml |
| b |
| diff -r 66f992977578 -r 121110a12cc9 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Tue Nov 14 15:02:18 2017 -0500 +++ b/bowtie2_wrapper.xml Fri Nov 24 07:44:07 2017 -0500 |
| [ |
| b'@@ -1,324 +1,327 @@\n-<tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01">\n+<tool id="bowtie2" name="Bowtie2" version="2.3.3.1" profile="17.01">\n <description>- map reads against reference genome</description>\n <macros>\n <import>bowtie2_macros.xml</import>\n </macros>\n <requirements>\n- <requirement type="package" version="2.3.2">bowtie2</requirement>\n- <requirement type="package" version="1.3.1">samtools</requirement>\n+ <requirement type="package" version="2.3.3.1">bowtie2</requirement>\n+ <requirement type="package" version="1.6">samtools</requirement>\n </requirements>\n <version_command>bowtie2 --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n- ## prepare bowtie2 index\n- #set index_path = \'\'\n- #if str($reference_genome.source) == "history":\n- bowtie2-build --threads \\${GALAXY_SLOTS:-4} \'$reference_genome.own_file\' genome &&\n- ln -s -f \'$reference_genome.own_file\' genome.fa &&\n- #set index_path = \'genome\'\n- #else:\n- #set index_path = $reference_genome.index.fields.path\n- #end if\n+## prepare bowtie2 index\n+#set index_path = \'\'\n+#if str($reference_genome.source) == "history":\n+ bowtie2-build --threads \\${GALAXY_SLOTS:-4} \'$reference_genome.own_file\' genome &&\n+ ln -s -f \'$reference_genome.own_file\' genome.fa &&\n+ #set index_path = \'genome\'\n+#else:\n+ #set index_path = $reference_genome.index.fields.path\n+#end if\n \n- ## Link in the input files, so bowtie2 can tell their type\n+## Link in the input files, so bowtie2 can tell their type\n \n- #set compressed="False"\n- #set reads_are_fastq = True\n- #if str($library.type) == \'paired\':\n- #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_f.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_f.fastq.bz2"\n- #set compressed = "BZ2"\n- #else if $library.input_1.is_of_type(\'fasta\'):\n- #set reads_are_fastq = False\n- #set read1 = "input_f.fasta"\n- #else:\n- #set read1 = "input_f.fastq"\n- #end if\n- ln -f -s \'${library.input_1}\' ${read1} &&\n+#set compressed="False"\n+#set reads_are_fastq = True\n+#if str($library.type) == \'paired\':\n+ #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else if $library.input_1.is_of_type(\'fasta\'):\n+ #set reads_are_fastq = False\n+ #set read1 = "input_f.fasta"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -f -s \'${library.input_1}\' ${read1} &&\n \n- #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = "input_r.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = "input_r.fastq.bz2"\n- #set compressed = "BZ2"\n- #else if $library.input_2.is_of_type(\'fasta\'):\n- #set read2 = "input_r.fasta"\n- #else:\n- #set read2 = "input_r.fastq"\n- #end if\n- ln -f -s \'${library.input_2}\' ${read2} &&\n- #else if str($library.type) == \'paired_collection\':\n- #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_f.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_f.fastq.bz2"\n- '..b' <expand macro="align_unalign" />\n <expand macro="paired_end_options" />\n-\n </when>\n </conditional>\n-\n <!-- reference genome -->\n <conditional name="reference_genome">\n <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">\n@@ -379,7 +373,6 @@\n <param name="own_file" type="data" format="fasta" label="Select reference genome" />\n </when>\n </conditional>\n-\n <!-- read group settings -->\n <expand macro="read_group_conditional" />\n <conditional name="analysis_type">\n@@ -502,7 +495,6 @@\n <!-- do nothing -->\n </when>\n </conditional>\n-\n <conditional name="sam_options">\n <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information">\n <option value="yes">Yes</option>\n@@ -511,6 +503,9 @@\n <when value="yes">\n <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>\n <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>\n+ <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>\n+ <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use \'=\'/\'X\', instead of \'M,\' to specify matches/mismatches in SAM record."/>\n+ <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>\n </when>\n <when value="no">\n <!-- do nothing -->\n@@ -535,11 +530,8 @@\n </conditional>\n <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />\n </inputs>\n-\n <!-- define outputs -->\n-\n <outputs>\n-\n <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >\n <filter>library[\'unaligned_file\'] is True</filter>\n <actions>\n@@ -618,7 +610,6 @@\n </conditional>\n </actions>\n </data>\n-\n <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">\n <filter>analysis_type[\'analysis_type_selector\'] == "simple" or analysis_type[\'sam_opt\'] is False</filter>\n <actions>\n@@ -639,7 +630,6 @@\n </conditional>\n </actions>\n </data>\n-\n <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">\n <filter>analysis_type[\'analysis_type_selector\'] == "full" and analysis_type[\'sam_opt\'] is True</filter>\n <actions>\n@@ -663,9 +653,7 @@\n <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">\n <filter>save_mapping_stats is True</filter>\n </data>\n-\n </outputs>\n-\n <tests>\n <test>\n <!-- test on paired-end datasets -->\n@@ -779,7 +767,6 @@\n <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>\n </test>\n </tests>\n-\n <help><![CDATA[\n **Bowtie2 Overview**\n \n' |