Mercurial > repos > wolma > mimodd_core
comparison 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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| 0:aa82b2e54055 | 1:1425ea794026 |
|---|---|
| 39 | 39 |
| 40 <inputs> | 40 <inputs> |
| 41 <param name="rg_id" type="text" size="80" | 41 <param name="rg_id" type="text" size="80" |
| 42 label="read-group ID (required)"> | 42 label="read-group ID (required)"> |
| 43 <validator type="empty_field" /> | 43 <validator type="empty_field" /> |
| 44 <sanitizer invalid_char=""> | 44 <expand macro="lex_sam_header" /> |
| 45 <valid initial="string.printable"> | |
| 46 <remove value=""" /> | |
| 47 </valid> | |
| 48 <mapping initial="none"> | |
| 49 <add source=""" target="\""/> | |
| 50 </mapping> | |
| 51 </sanitizer> | |
| 52 </param> | 45 </param> |
| 53 <param name="rg_sm" type="text" size="80" | 46 <param name="rg_sm" type="text" size="80" |
| 54 label="sample name (required)"> | 47 label="sample name (required)"> |
| 55 <validator type="empty_field" /> | 48 <validator type="empty_field" /> |
| 56 <sanitizer invalid_char=""> | 49 <expand macro="lex_sam_header" /> |
| 57 <valid initial="string.printable"> | |
| 58 <remove value=""" /> | |
| 59 </valid> | |
| 60 <mapping initial="none"> | |
| 61 <add source=""" target="\""/> | |
| 62 </mapping> | |
| 63 </sanitizer> | |
| 64 </param> | 50 </param> |
| 65 <param name="rg_ds" type="text" size="80" label="description"> | 51 <param name="rg_ds" type="text" size="80" label="description"> |
| 66 <sanitizer invalid_char=""> | 52 <expand macro="lex_sam_header" /> |
| 67 <valid initial="string.printable"> | |
| 68 <remove value=""" /> | |
| 69 </valid> | |
| 70 <mapping initial="none"> | |
| 71 <add source=""" target="\""/> | |
| 72 </mapping> | |
| 73 </sanitizer> | |
| 74 </param> | 53 </param> |
| 75 <param name="rg_date" type="text" | 54 <param name="rg_date" type="text" |
| 76 label="date (YYYY-MM-DD) the run was produced"> | 55 label="date (YYYY-MM-DD) the run was produced"> |
| 77 <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> | 56 <expand macro="YYYY-MM-DD_format_validator" /> |
| 78 </param> | 57 </param> |
| 79 <param name="rg_cn" type="text" size="80" | 58 <param name="rg_cn" type="text" size="80" |
| 80 label="name of sequencing center"> | 59 label="name of sequencing center"> |
| 81 <sanitizer invalid_char=""> | 60 <expand macro="lex_sam_header" /> |
| 82 <valid initial="string.printable"> | |
| 83 <remove value=""" /> | |
| 84 </valid> | |
| 85 <mapping initial="none"> | |
| 86 <add source=""" target="\""/> | |
| 87 </mapping> | |
| 88 </sanitizer> | |
| 89 </param> | 61 </param> |
| 90 <param name="rg_lb" type="text" size="80" label="read-group library"> | 62 <param name="rg_lb" type="text" size="80" label="read-group library"> |
| 91 <sanitizer invalid_char=""> | 63 <expand macro="lex_sam_header" /> |
| 92 <valid initial="string.printable"> | |
| 93 <remove value=""" /> | |
| 94 </valid> | |
| 95 <mapping initial="none"> | |
| 96 <add source=""" target="\""/> | |
| 97 </mapping> | |
| 98 </sanitizer> | |
| 99 </param> | 64 </param> |
| 100 <param name="rg_pl" type="text" | 65 <param name="rg_pl" type="text" |
| 101 label="platform/technology used to produce the reads"> | 66 label="platform/technology used to produce the reads"> |
| 102 <option value="ILLUMINA">ILLUMINA</option> | 67 <expand macro="known_sequencing_platform options" /> |
| 103 <option value="PACBIO">PACBIO</option> | 68 <expand macro="lex_sam_header" /> |
| 104 <option value="IONTORRENT">IONTORRENT</option> | |
| 105 <option value="ONT">ONT</option> | |
| 106 <option value="LS454">LS454</option> | |
| 107 <option value="SOLID">SOLID</option> | |
| 108 <option value="HELICOS">HELICOS</option> | |
| 109 <option value="CAPILLARY">CAPILLARY</option> | |
| 110 </param> | 69 </param> |
| 111 <param name="rg_pi" type="text" label="predicted median insert size" /> | 70 <param name="rg_pi" type="text" label="predicted median insert size"> |
| 71 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> | |
| 72 </param> | |
| 112 <param name="rg_pu" type="text" size="80" | 73 <param name="rg_pu" type="text" size="80" |
| 113 label="platform unit; unique identifier"> | 74 label="platform unit; unique identifier"> |
| 114 <sanitizer invalid_char=""> | 75 <expand macro="lex_sam_header" /> |
| 115 <valid initial="string.printable"> | |
| 116 <remove value=""" /> | |
| 117 </valid> | |
| 118 <mapping initial="none"> | |
| 119 <add source=""" target="\""/> | |
| 120 </mapping> | |
| 121 </sanitizer> | |
| 122 </param> | 76 </param> |
| 123 </inputs> | 77 </inputs> |
| 124 | 78 |
| 125 <outputs> | 79 <outputs> |
| 126 <data name="ofile" format="sam" | 80 <data name="ofile" format="sam" |