Mercurial > repos > wolma > mimodd_core
diff sam_header.xml @ 1:1425ea794026 draft default tip
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
| author | wolma |
|---|---|
| date | Mon, 18 Dec 2017 03:39:07 -0500 |
| parents | aa82b2e54055 |
| children |
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--- a/sam_header.xml Sat Nov 11 18:19:22 2017 -0500 +++ b/sam_header.xml Mon Dec 18 03:39:07 2017 -0500 @@ -41,84 +41,38 @@ <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> + <expand macro="lex_sam_header" /> </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> + <expand macro="lex_sam_header" /> </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> + <expand macro="lex_sam_header" /> </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> + <expand macro="YYYY-MM-DD_format_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> + <expand macro="lex_sam_header" /> </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> + <expand macro="lex_sam_header" /> </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> + <expand macro="known_sequencing_platform options" /> + <expand macro="lex_sam_header" /> </param> - <param name="rg_pi" type="text" label="predicted median insert size" /> + <param name="rg_pi" type="text" label="predicted median insert size"> + <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> + </param> <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> + <expand macro="lex_sam_header" /> </param> </inputs>