Mercurial > repos > wolma > mimodd_ngs_run_annotation
changeset 0:b2bc4e918462 draft
Uploaded
| author | wolma |
|---|---|
| date | Thu, 14 Aug 2014 09:57:49 -0400 |
| parents | |
| children | 623cf7b461fa |
| files | sam_header.xml |
| diffstat | 1 files changed, 129 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_header.xml Thu Aug 14 09:57:49 2014 -0400 @@ -0,0 +1,129 @@ +<tool id="sam_header" 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> + </requirements> + <command> + mimodd header + + --rg_id "$rg_id" + --rg_sm "$rg_sm" + + #if $str($rg_cn): + --rg_cn "$rg_cn" + #end if + #if $str($rg_ds): + --rg_ds "$rg_ds" + #end if + #if $str($anno) and $str($month) and $str($day): + --rg_dt "$anno-$month-$day" + #end if + #if $str($rg_lb): + --rg_lb "$rg_lb" + #end if + #if $str($rg_pl): + --rg_pl "$rg_pl" + #end if + #if $str($rg_ds): + --rg_pi "$rg_pi" + #end if + #if $str($rg_pu): + --rg_pu "$rg_pu" + #end if + + --outputfile $outputfile + + </command> + + <inputs> + <param name="rg_id" type="text" size="80" label="read-group ID (mandatory)"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </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"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_ds" type="text" size="80" label="description"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </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_lb" type="text" size="80" label="read-group library"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <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"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <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}"/> + </outputs> + +<help> +.. class:: infomark + + **What it does** + +This tool takes the user-provided information about a next-generation sequencing run and constructs a valid header in the SAM file format from it. + +The result file can be used by the tools *Convert* and *Reheader* or in the *SNAP Read Alignment* step to add run metadata to sequenced reads files (or to overwrite pre-existing information). + +**Note:** + +**MiModD requires run metadata for every input file at the Alignment step !** + +**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. + +</help> +</tool> +