| Previous changeset 27:a6d65b0c67af (2021-07-10) Next changeset 29:f6877ad76b00 (2022-07-06) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a" |
|
modified:
bowtie2_macros.xml bowtie2_wrapper.xml |
| b |
| diff -r a6d65b0c67af -r cd659e8cc5fa bowtie2_macros.xml --- a/bowtie2_macros.xml Sat Jul 10 07:45:14 2021 +0000 +++ b/bowtie2_macros.xml Mon Jan 31 08:31:43 2022 +0000 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.4.2</token> + <token name="@TOOL_VERSION@">2.4.5</token> <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> |
| b |
| diff -r a6d65b0c67af -r cd659e8cc5fa bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Sat Jul 10 07:45:14 2021 +0000 +++ b/bowtie2_wrapper.xml Mon Jan 31 08:31:43 2022 +0000 |
| [ |
| @@ -1,11 +1,14 @@ <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05"> <description>- map reads against reference genome</description> + <xrefs> + <xref type="bio.tools">bowtie2</xref> + </xrefs> <macros> <import>bowtie2_macros.xml</import> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> - <requirement type="package" version="1.11">samtools</requirement> + <requirement type="package" version="1.14">samtools</requirement> </requirements> <version_command>bowtie2 --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -659,7 +662,7 @@ <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="3"> <!-- test on list paired collection --> @@ -675,7 +678,7 @@ </collection> </param> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="1"> <!-- test on paired-end datasets with read group info --> @@ -690,7 +693,7 @@ <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="2"> <!-- test on paired-end datasets with stats output --> @@ -703,7 +706,7 @@ <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> <param name="own_file" value="bowtie2-ref.fasta" /> <param name="save_mapping_stats" value="true" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> <output name="mapping_stats"> <assert_contents> <has_text text="of these" /> @@ -722,7 +725,7 @@ <param name="source" value="history" /> <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="1"> <!-- test on fastqsanger.gz paired-end datasets --> @@ -734,7 +737,7 @@ <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="1"> <!-- test on fastqsanger.bz2 paired-end datasets --> @@ -746,7 +749,7 @@ <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="1"> <!-- test on fasta paired-end datasets --> @@ -758,7 +761,7 @@ <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> + <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/> </test> <test expect_num_outputs="1"> <!-- test on fasta paired-end datasets with bam_native as output --> |