Mercurial > repos > devteam > bowtie2
changeset 31:0d4acadabb04 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit f25b49ba5f2f3e5542e75224948818c32dea920a
| author | iuc |
|---|---|
| date | Mon, 26 Feb 2024 08:50:20 +0000 |
| parents | 03e9b2fbc005 |
| children | |
| files | bowtie2_macros.xml bowtie2_wrapper.xml test-data/bowtie2-test1.bam test-data/bowtie2-test2.bam test-data/bowtie2-test_fasta_in.bam test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam test-data/bowtie2-test_il.bam |
| diffstat | 7 files changed, 17 insertions(+), 18 deletions(-) [+] |
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--- a/bowtie2_macros.xml Thu Nov 03 19:37:50 2022 +0000 +++ b/bowtie2_macros.xml Mon Feb 26 08:50:20 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.5.0</token> + <token name="@TOOL_VERSION@">2.5.3</token> <token name="@VERSION_SUFFIX@">0</token> <!-- Import this at the top of your command block and then define rg_auto_name. --> @@ -310,11 +310,11 @@ <option value="--rf">--rf</option> <option value="--ff">--ff</option> </param> - <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> - <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> - <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> - <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> - <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> + <param argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> + <param argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> + <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> + <param argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> + <param argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> </when> <when value="no"> <!-- do nothing -->
--- a/bowtie2_wrapper.xml Thu Nov 03 19:37:50 2022 +0000 +++ b/bowtie2_wrapper.xml Mon Feb 26 08:50:20 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> +<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> @@ -8,7 +8,7 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> - <requirement type="package" version="1.16.1">samtools</requirement> + <requirement type="package" version="1.19.2">samtools</requirement> </requirements> <version_command>bowtie2 --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -68,7 +68,7 @@ #else: #set read1 = "input_f.fastq" #end if - ln -s '${library.input_1.forward}' ${read1} && + ln -f -s '${library.input_1.forward}' ${read1} && #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): #set read2 = "input_r.fastq.gz" @@ -81,7 +81,7 @@ #else: #set read2 = "input_r.fastq" #end if - ln -s '${library.input_1.reverse}' ${read2} && + ln -f -s '${library.input_1.reverse}' ${read2} && #else if str($library.type) == 'paired_interleaved': #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): @@ -96,7 +96,7 @@ #else: #set read1 = "input_il.fastq" #end if - ln -s '${library.input_1}' ${read1} && + ln -f -s '${library.input_1}' ${read1} && #else: #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" @@ -110,7 +110,7 @@ #else: #set read1 = "input_f.fastq" #end if - ln -s '${library.input_1}' ${read1} && + ln -f -s '${library.input_1}' ${read1} && #end if ## execute bowtie2 @@ -339,7 +339,6 @@ <option value="paired_collection">Paired-end Dataset Collection</option> <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> </param> - <when value="single"> <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> <expand macro="align_unalign" /> @@ -523,12 +522,12 @@ </param> <when value="yes"> <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."/> - <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"/> - <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"/> - <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"/> + <param argument="--no-unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> + <param argument="--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"/> + <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"/> <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/> - <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"/> - <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" + <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> + <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Reorder output to reflect order of the input file" 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." /> </when>