Mercurial > repos > wolma > mimodd
diff sam_header.xml @ 23:5db0545b9004 draft
update to v0.1.7.3
author | wolma |
---|---|
date | Thu, 21 Jul 2016 03:55:49 -0400 |
parents | c46406466625 |
children |
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--- a/sam_header.xml Sun Jun 12 07:39:46 2016 -0400 +++ b/sam_header.xml Thu Jul 21 03:55:49 2016 -0400 @@ -1,9 +1,9 @@ -<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.2"> +<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.3"> <description>Create a SAM format header from run metadata for sample annotation.</description> <macros> <import>toolshed_macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements" /> <version_command>python3 -m MiModD version -q</version_command> <command> python3 -m MiModD header @@ -38,73 +38,73 @@ </command> <inputs> - <param name="rg_id" type="text" size="80" label="read-group ID (required)"> + <param label="read-group ID (required)" name="rg_id" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> - <param name="rg_sm" type="text" size="80" label="sample name (required)"> + <param label="sample name (required)" name="rg_sm" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> - <param name="rg_ds" type="text" size="80" label="description"> + <param label="description" name="rg_ds" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> - <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" /> - <param name="rg_cn" type="text" size="80" label="name of sequencing center"> + <param label="date (YYYY-MM-DD) the run was produced" name="rg_date" type="text" /> + <param label="name of sequencing center" name="rg_cn" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> - <param name="rg_lb" type="text" size="80" label="read-group library"> + <param label="read-group library" name="rg_lb" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> - <param name="rg_pl" type="text" label="platform/technology used to produce the reads" /> - <param name="rg_pi" type="text" label="predicted median insert size" /> - <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier"> + <param label="platform/technology used to produce the reads" name="rg_pl" type="text" /> + <param label="predicted median insert size" name="rg_pi" type="text" /> + <param label="platform unit; unique identifier" name="rg_pu" size="80" type="text"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> </valid> <mapping initial="none"> - <add source=""" target="\""/> + <add source=""" target="\"" /> </mapping> </sanitizer> </param> </inputs> <outputs> - <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> + <data format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}" name="outputfile" /> </outputs> <help> @@ -125,5 +125,4 @@ While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming, this practice protects against information loss and ensures that the input datasets will remain useful for others in the future. </help> -</tool> - +</tool> \ No newline at end of file