Mercurial > repos > dfornika > artic_align_trim
changeset 7:97b21fddeff7 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
author | dfornika |
---|---|
date | Tue, 10 Mar 2020 23:20:08 +0000 |
parents | 26516cf26444 |
children | e015f2244d4f |
files | artic_align_trim.xml |
diffstat | 1 files changed, 19 insertions(+), 9 deletions(-) [+] |
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--- a/artic_align_trim.xml Tue Mar 10 22:52:48 2020 +0000 +++ b/artic_align_trim.xml Tue Mar 10 23:20:08 2020 +0000 @@ -6,13 +6,20 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ python '${__tool_directory__}/align_trim.py' - '${primer_scheme_bedfile.fields.path}' - --start - --report '${start_trim_report}' - < '${input_alignment}' - 2> '${start_trim_err}' | + '${primer_scheme_bedfile.fields.path}' + --start + --report '${start_trim_report}' + < '${input_alignment}' + 2> '${start_trim_err}' | samtools view -bS - | - samtools sort - -o '${trimmed_sorted_alignment}' + samtools sort - -o '${start_trimmed_sorted_alignment}' && + python '${__tool_directory__}/align_trim.py' + '${primer_scheme_bedfile.fields.path}' + --report '${end_trim_report}' + < '${input_alignment}' + 2> '${end_trim_err}' | + samtools view -bS - | + samtools sort - -o '${end_trimmed_sorted_alignment}' && ]]></command> <inputs> <param name="input_alignment" type="data" format="bam" label="Input Alignment"/> @@ -23,9 +30,12 @@ </param> </inputs> <outputs> - <data name="start_trim_report" format="txt" label="Alignment Report" /> - <data name="start_trim_err" format="txt" label="Alignment Error Report" /> - <data name="trimmed_sorted_alignment" format="bam" /> + <data name="start_trim_report" format="txt" label="Report (Trim to start of primers)" /> + <data name="start_trim_err" format="txt" label="Error Report (Trim to start of primers)" /> + <data name="end_trim_report" format="txt" label="Report (Trim to end of primers)" /> + <data name="end_trim_err" format="txt" label="Error Report (Trim to end of primers)" /> + <data name="start_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to start of primers)" /> + <data name="end_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to end of primers)" /> </outputs> <tests> </tests>