Mercurial > repos > wolma > mimodd
annotate sam_header.xml @ 18:2742ad4d1608 draft
rebase on package_python_3_4_lean
| author | wolma |
|---|---|
| date | Tue, 26 Apr 2016 11:21:43 -0400 |
| parents | 93db2f9bca12 |
| children | c46406466625 |
| rev | line source |
|---|---|
|
9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
|
1 <tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.2"> |
| 0 | 2 <description>Create a SAM format header from run metadata for sample annotation.</description> |
| 2 | 3 <macros> |
| 4 <import>toolshed_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 0 | 7 <version_command>mimodd version -q</version_command> |
| 8 <command> | |
| 9 mimodd header | |
| 10 | |
| 11 --rg-id "$rg_id" | |
| 12 --rg-sm "$rg_sm" | |
| 13 | |
| 14 #if $str($rg_cn): | |
| 15 --rg-cn "$rg_cn" | |
| 16 #end if | |
| 17 #if $str($rg_ds): | |
| 18 --rg-ds "$rg_ds" | |
| 19 #end if | |
| 20 #if $str($rg_date): | |
| 21 --rg-dt "$rg_date" | |
| 22 #end if | |
| 23 #if $str($rg_lb): | |
| 24 --rg-lb "$rg_lb" | |
| 25 #end if | |
| 26 #if $str($rg_pl): | |
| 27 --rg-pl "$rg_pl" | |
| 28 #end if | |
| 29 #if $str($rg_pi): | |
| 30 --rg-pi "$rg_pi" | |
| 31 #end if | |
| 32 #if $str($rg_pu): | |
| 33 --rg-pu "$rg_pu" | |
| 34 #end if | |
| 35 | |
| 36 --ofile "$outputfile" | |
| 37 | |
| 38 </command> | |
| 39 | |
| 40 <inputs> | |
| 41 <param name="rg_id" type="text" size="80" label="read-group ID (required)"> | |
| 42 <sanitizer invalid_char=""> | |
| 43 <valid initial="string.printable"> | |
| 44 <remove value=""" /> | |
| 45 </valid> | |
| 46 <mapping initial="none"> | |
| 47 <add source=""" target="\""/> | |
| 48 </mapping> | |
| 49 </sanitizer> | |
| 50 </param> | |
| 51 <param name="rg_sm" type="text" size="80" label="sample name (required)"> | |
| 52 <sanitizer invalid_char=""> | |
| 53 <valid initial="string.printable"> | |
| 54 <remove value=""" /> | |
| 55 </valid> | |
| 56 <mapping initial="none"> | |
| 57 <add source=""" target="\""/> | |
| 58 </mapping> | |
| 59 </sanitizer> | |
| 60 </param> | |
| 61 <param name="rg_ds" type="text" size="80" label="description"> | |
| 62 <sanitizer invalid_char=""> | |
| 63 <valid initial="string.printable"> | |
| 64 <remove value=""" /> | |
| 65 </valid> | |
| 66 <mapping initial="none"> | |
| 67 <add source=""" target="\""/> | |
| 68 </mapping> | |
| 69 </sanitizer> | |
| 70 </param> | |
| 71 <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" /> | |
| 72 <param name="rg_cn" type="text" size="80" label="name of sequencing center"> | |
| 73 <sanitizer invalid_char=""> | |
| 74 <valid initial="string.printable"> | |
| 75 <remove value=""" /> | |
| 76 </valid> | |
| 77 <mapping initial="none"> | |
| 78 <add source=""" target="\""/> | |
| 79 </mapping> | |
| 80 </sanitizer> | |
| 81 </param> | |
| 82 <param name="rg_lb" type="text" size="80" label="read-group library"> | |
| 83 <sanitizer invalid_char=""> | |
| 84 <valid initial="string.printable"> | |
| 85 <remove value=""" /> | |
| 86 </valid> | |
| 87 <mapping initial="none"> | |
| 88 <add source=""" target="\""/> | |
| 89 </mapping> | |
| 90 </sanitizer> | |
| 91 </param> | |
| 92 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" /> | |
| 93 <param name="rg_pi" type="text" label="predicted median insert size" /> | |
| 94 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier"> | |
| 95 <sanitizer invalid_char=""> | |
| 96 <valid initial="string.printable"> | |
| 97 <remove value=""" /> | |
| 98 </valid> | |
| 99 <mapping initial="none"> | |
| 100 <add source=""" target="\""/> | |
| 101 </mapping> | |
| 102 </sanitizer> | |
| 103 </param> | |
| 104 </inputs> | |
| 105 | |
| 106 <outputs> | |
| 107 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> | |
| 108 </outputs> | |
| 109 | |
| 110 <help> | |
| 111 .. class:: infomark | |
| 112 | |
| 113 **What it does** | |
| 114 | |
| 115 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. | |
| 116 | |
| 117 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). | |
| 118 | |
| 119 **Note:** | |
| 120 | |
| 121 **MiModD requires run metadata for every input file at the Alignment step !** | |
| 122 | |
| 123 **Tip:** | |
| 124 | |
| 125 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. | |
| 126 | |
| 127 </help> | |
| 128 </tool> | |
| 129 |