| Next changeset 1:25ca5d73aedf (2021-08-27) |
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Commit message:
"planemo upload for repository https://github.com/davebx/bellerophon commit 5fe46c36adac4843cd548802073aa62b0afc61cd" |
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added:
bellerophon.xml test-data/forward.bam test-data/forward.sam test-data/merged-out.bam test-data/merged-sam.bam test-data/reverse.bam test-data/reverse.sam |
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| diff -r 000000000000 -r eca6296a091a bellerophon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bellerophon.xml Fri May 28 20:54:47 2021 +0000 |
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| @@ -0,0 +1,64 @@ +<tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>chimeric reads from Arima Genomics</description> + <macros> + <token name="@TOOL_VERSION@">1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement> + <requirement type="package" version="1.12">samtools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $forward.is_of_type("sam"): + #set $forward_input = 'forward_input.sam' + ln -s '${forward}' '$forward_input' && + #else: + #set $forward_input = 'forward_input.bam' + ln -s '${forward}' '$forward_input' && + #end if + #if $reverse.is_of_type("sam"): + #set $reverse_input = 'reverse_input.sam' + ln -s '${reverse}' '$reverse_input' && + #else: + #set $reverse_input = 'reverse_input.bam' + ln -s '${reverse}' '$reverse_input' && + #end if + bellerophon + --forward $forward_input + --reverse $reverse_input + --quality $quality + --output 'merged_out.bam' + && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam + ]]> + </command> + <inputs> + <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads" + help="This is usually the forward reads in your experiment." /> + <param argument="--reverse" type="data" format="qname_sorted.bam,sam" label="Second set of reads" + help="This is usually the reverse reads in your experiment." /> + <param argument="--quality" type="integer" value="20" label="Minimum mapping quality"/> + </inputs> + <outputs> + <data name="outfile" format="bam"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="forward" value="forward.bam" ftype="qname_sorted.bam" /> + <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" /> + <param name="quality" value="20" /> + <output name="outfile" file="merged-out.bam" ftype="bam" /> + </test> + <test expect_num_outputs="1"> + <param name="forward" value="forward.sam" ftype="sam" /> + <param name="reverse" value="reverse.sam" ftype="sam" /> + <param name="quality" value="12" /> + <output name="outfile" file="merged-sam.bam" ftype="bam" /> + </test> + </tests> + <help><![CDATA[ + Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics. + ]]></help> + <citations> + <citation type="doi">10.1038/s41586-021-03451-0</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r eca6296a091a test-data/forward.bam |
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| Binary file test-data/forward.bam has changed |
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| diff -r 000000000000 -r eca6296a091a test-data/forward.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/forward.sam Fri May 28 20:54:47 2021 +0000 |
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| diff -r 000000000000 -r eca6296a091a test-data/reverse.bam |
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| Binary file test-data/reverse.bam has changed |
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| diff -r 000000000000 -r eca6296a091a test-data/reverse.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reverse.sam Fri May 28 20:54:47 2021 +0000 |
| b |
| b'@@ -0,0 +1,2541 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|