Mercurial > repos > devteam > picard
changeset 23:4740a2548206 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 07:58:57 +0000 |
| parents | 81de93de916f |
| children | e65f2d5fd3d8 |
| files | picard_FastqToSam.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml |
| diffstat | 4 files changed, 40 insertions(+), 28 deletions(-) [+] |
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--- a/picard_FastqToSam.xml Wed Feb 19 19:26:15 2020 +0000 +++ b/picard_FastqToSam.xml Wed Sep 01 07:58:57 2021 +0000 @@ -1,11 +1,14 @@ <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>convert Fastq data into unaligned BAM</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <description>convert Fastq data into unaligned BAM</description> + <xrefs> + <xref type="bio.tools">picard_fastqtosam</xref> + </xrefs> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">1</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ @java_options@ picard FastqToSam
--- a/picard_ReorderSam.xml Wed Feb 19 19:26:15 2020 +0000 +++ b/picard_ReorderSam.xml Wed Sep 01 07:58:57 2021 +0000 @@ -1,11 +1,14 @@ <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>reorder reads to match ordering in reference sequences</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <description>reorder reads to match ordering in reference sequences</description> + <xrefs> + <xref type="bio.tools">picard_reordersam</xref> + </xrefs> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">1</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ #set $picard_dict = "localref.dict"
--- a/picard_ReplaceSamHeader.xml Wed Feb 19 19:26:15 2020 +0000 +++ b/picard_ReplaceSamHeader.xml Wed Sep 01 07:58:57 2021 +0000 @@ -1,11 +1,14 @@ <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>replace header in a SAM/BAM dataset</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <description>replace header in a SAM/BAM dataset</description> + <xrefs> + <xref type="bio.tools">picard_replacesamheader</xref> + </xrefs> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">1</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@
--- a/picard_SamToFastq.xml Wed Feb 19 19:26:15 2020 +0000 +++ b/picard_SamToFastq.xml Wed Sep 01 07:58:57 2021 +0000 @@ -1,11 +1,14 @@ <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> + <xrefs> + <xref type="bio.tools">picard_samtofastq</xref> + </xrefs> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">2</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@