| Previous changeset 21:3ba8d4563129 (2018-04-10) Next changeset 23:17062a0decb7 (2018-06-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32 |
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modified:
bowtie2_wrapper.xml |
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added:
test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam |
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| diff -r 3ba8d4563129 -r c3dd1aeb7d07 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Tue Apr 10 18:40:49 2018 -0400 +++ b/bowtie2_wrapper.xml Thu Apr 12 17:42:40 2018 -0400 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">\n+<tool id="bowtie2" name="Bowtie2" version="2.3.4.2" profile="18.01">\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="2.3.4">bowtie2</requirement>\n- <requirement type="package" version="1.6">samtools</requirement>\n+ <requirement type="package" version="1.8">samtools</requirement>\n </requirements>\n <version_command>bowtie2 --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -280,15 +280,6 @@\n -D ${analysis_type.effort_options.D}\n -R ${analysis_type.effort_options.R}\n #end if\n-\n- #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":\n- ${analysis_type.sam_options.no_unal}\n- ${analysis_type.sam_options.omit_sec_seq}\n- ${analysis_type.sam_options.sam_no_qname_trunc}\n- ${analysis_type.sam_options.xeq}\n- ${analysis_type.sam_options.soft_clipped_unmapped_tlen}\n- #end if\n-\n #if str( $analysis_type.other_options.other_options_selector ) == "yes":\n ${analysis_type.other_options.reorder}\n ${analysis_type.other_options.non_deterministic}\n@@ -299,15 +290,26 @@\n ${analysis_type.cline}\n #end if\n \n+#if str( $sam_options.sam_options_selector ) == "yes":\n+ ${sam_options.no_unal}\n+ ${sam_options.omit_sec_seq}\n+ ${sam_options.sam_no_qname_trunc}\n+ ${sam_options.xeq}\n+ ${sam_options.soft_clipped_unmapped_tlen}\n+ ${sam_options.reorder}\n+#end if\n+\n ## mapping stats (i.e. stderr from bowtie2)\n #if $save_mapping_stats\n 2> \'$mapping_stats\'\n #end if\n \n ## output file\n-#if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):\n+#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == \'\'):\n | samtools sort -@\\${GALAXY_SLOTS:-2} -O bam -o \'$output\'\n-#else\n+#else if $sam_options.reorder:\n+ | samtools view -bS - -o \'$output\'\n+#else:\n > \'$output_sam\'\n #end if\n \n@@ -497,29 +499,13 @@\n <!-- do nothing -->\n </when>\n </conditional>\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- <option value="no" selected="true">No</option>\n- </param>\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 name="sam_no_qname_trunc" 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 name="soft_clipped_unmapped_tlen" 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- '..b' want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information">\n+ <option value="yes">Yes</option>\n+ <option value="no" selected="true">No</option>\n+ </param>\n+ <when value="yes">\n <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>\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 name="sam_no_qname_trunc" 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 name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>\n+ <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""\n+ label="Reorder output to reflect order of the input file"\n+ help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />\n </when>\n+ <when value="no"/>\n </conditional>\n <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />\n </inputs>\n@@ -612,8 +615,11 @@\n </conditional>\n </actions>\n </data>\n- <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">\n+ <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">\n <filter>analysis_type[\'analysis_type_selector\'] == "simple" or analysis_type[\'sam_opt\'] is False</filter>\n+ <change_format>\n+ <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />\n+ </change_format>\n <actions>\n <conditional name="reference_genome.source">\n <when value="indexed">\n@@ -768,6 +774,20 @@\n <param name="own_file" value="bowtie2-ref.fasta" />\n <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>\n </test>\n+ <test>\n+ <!-- test on fasta paired-end datasets with bam_native as output -->\n+ <param name="type" value="paired"/>\n+ <param name="paired_options_selector" value="no"/>\n+ <param name="unaligned_file" value="false"/>\n+ <param name="analysis_type_selector" value="simple"/>\n+ <param name="source" value="history" />\n+ <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>\n+ <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>\n+ <param name="own_file" value="bowtie2-ref.fasta" />\n+ <param name="sam_options_selector" value="yes" />\n+ <param name="reorder" value="true" />\n+ <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n **Bowtie2 Overview**\n' |
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| diff -r 3ba8d4563129 -r c3dd1aeb7d07 test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam |
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| Binary file test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam has changed |