Mercurial > repos > wolma > mimodd_tool_wrappers
diff sam_header.xml @ 3:d6ec32ce882b draft default tip
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| author | wolma |
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| date | Tue, 28 Mar 2017 04:34:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_header.xml Tue Mar 28 04:34:04 2017 -0400 @@ -0,0 +1,128 @@ +<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" /> + <version_command>mimodd version -q</version_command> + <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 $str($rg_date): + --rg-dt "$rg_date" + #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_pi): + --rg-pi "$rg_pi" + #end if + #if $str($rg_pu): + --rg-pu "$rg_pu" + #end if + + --ofile "$outputfile" + + </command> + + <inputs> + <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="\"" /> + </mapping> + </sanitizer> + </param> + <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="\"" /> + </mapping> + </sanitizer> + </param> + <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="\"" /> + </mapping> + </sanitizer> + </param> + <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="\"" /> + </mapping> + </sanitizer> + </param> + <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="\"" /> + </mapping> + </sanitizer> + </param> + <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="\"" /> + </mapping> + </sanitizer> + </param> + </inputs> + + <outputs> + <data format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}" name="outputfile" /> + </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, 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>