Mercurial > repos > wolma > mimodd_ngs_run_annotation
changeset 2:7bce49512bad draft
version 0_1_5
| author | wolma |
|---|---|
| date | Tue, 09 Dec 2014 16:28:20 -0500 |
| parents | 623cf7b461fa |
| children | 666266c4e81f |
| files | sam_header.xml |
| diffstat | 1 files changed, 29 insertions(+), 30 deletions(-) [+] |
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--- a/sam_header.xml Thu Aug 14 10:36:08 2014 -0400 +++ b/sam_header.xml Tue Dec 09 16:28:20 2014 -0500 @@ -1,42 +1,43 @@ -<tool id="sam_header" name="NGS Run Annotation"> +<tool id="ngs_run_annotation" name="NGS Run Annotation"> <description>Create a SAM format header from run metadata for sample annotation.</description> <requirements> - <requirement type="package" version="0.1.3">mimodd</requirement> + <requirement type="package" version="0.1.5">mimodd</requirement> </requirements> + <version_command>mimodd version -q</version_command> <command> mimodd header - --rg_id "$rg_id" - --rg_sm "$rg_sm" + --rg-id "$rg_id" + --rg-sm "$rg_sm" #if $str($rg_cn): - --rg_cn "$rg_cn" + --rg-cn "$rg_cn" #end if #if $str($rg_ds): - --rg_ds "$rg_ds" + --rg-ds "$rg_ds" #end if - #if $str($anno) and $str($month) and $str($day): - --rg_dt "$anno-$month-$day" + #if $str($rg_date): + --rg-dt "$rg_date" #end if #if $str($rg_lb): - --rg_lb "$rg_lb" + --rg-lb "$rg_lb" #end if #if $str($rg_pl): - --rg_pl "$rg_pl" + --rg-pl "$rg_pl" #end if - #if $str($rg_ds): - --rg_pi "$rg_pi" + #if $str($rg_pi): + --rg-pi "$rg_pi" #end if #if $str($rg_pu): - --rg_pu "$rg_pu" + --rg-pu "$rg_pu" #end if - --outputfile $outputfile + --ofile $outputfile </command> <inputs> - <param name="rg_id" type="text" size="80" label="read-group ID (mandatory)"> + <param name="rg_id" type="text" size="80" label="read-group ID (required)"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> @@ -46,17 +47,7 @@ </mapping> </sanitizer> </param> - <param name="rg_sm" type="text" size="80" label="sample name (mandatory)"> - <sanitizer invalid_char=""> - <valid initial="string.printable"> - <remove value=""" /> - </valid> - <mapping initial="none"> - <add source=""" target="\""/> - </mapping> - </sanitizer> - </param> - <param name="rg_cn" type="text" size="80" label="name of sequencing center"> + <param name="rg_sm" type="text" size="80" label="sample name (required)"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value=""" /> @@ -76,9 +67,17 @@ </mapping> </sanitizer> </param> - <param name="anno" type="text" label="year (YYYY) the run was produced" /> - <param name="month" type="text" label="month (MM) the run was produced" /> - <param name="day" type="text" label="day (DD) the run was produced" /> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> <param name="rg_lb" type="text" size="80" label="read-group library"> <sanitizer invalid_char=""> <valid initial="string.printable"> @@ -122,7 +121,7 @@ **Tip:** -While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, the **recommended approach** is 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. +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>