Mercurial > repos > wolma > mimodd_core
diff sam_header.xml @ 0:aa82b2e54055 draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
| author | wolma |
|---|---|
| date | Sat, 11 Nov 2017 18:19:22 -0500 |
| parents | |
| children | 1425ea794026 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_header.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,169 @@ +<tool id="mimodd_header" name="MiModD Run Annotation" version="@MIMODD_WRAPPER_VERSION@"> + <description> + writes run metadata in SAM format for attaching it to sequenced reads data + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + 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 '$rg_pu' + #end if + --ofile '$ofile' + + ]]></command> + + <inputs> + <param name="rg_id" type="text" size="80" + label="read-group ID (required)"> + <validator type="empty_field" /> + <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 (required)"> + <validator type="empty_field" /> + <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="rg_date" type="text" + label="date (YYYY-MM-DD) the run was produced"> + <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator> + </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_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"> + <option value="ILLUMINA">ILLUMINA</option> + <option value="PACBIO">PACBIO</option> + <option value="IONTORRENT">IONTORRENT</option> + <option value="ONT">ONT</option> + <option value="LS454">LS454</option> + <option value="SOLID">SOLID</option> + <option value="HELICOS">HELICOS</option> + <option value="CAPILLARY">CAPILLARY</option> + </param> + <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="ofile" format="sam" + label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="rg_id" value="000" /> + <param name="rg_sm" value="N2" /> + <param name="rg_ds" value="C. elegans wt" /> + <param name="rg_date" value="2017-06-27" /> + <param name="rg_cn" value="ABC" /> + <param name="rg_lb" value="XYZ" /> + <param name="rg_pl" value="ILLUMINA" /> + <param name="rg_pi" value="400" /> + <param name="rg_pu" value="SEQ123" /> + <output name="ofile" ftype="sam" file="header_only.sam" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +This tool takes user-provided information about a next-generation sequencing +run and constructs a valid SAM format header from it. + +The resulting dataset can be used by the *MiModD Convert*, *MiModD Reheader* +and the *MiModD Read Alignment* tool to add run metadata to sequenced reads +input datasets (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_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool> +