Mercurial > repos > lgueguen > sartools

comparison macros.xml @ 3:de6d0b7c17af draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
release 1.6.3
author lgueguen
date Mon, 01 Oct 2018 05:07:56 -0400
parents d86ccac2a660
children 05c9b1a7f44e
comparison
equal deleted inserted replaced
2:d86ccac2a660 3:de6d0b7c17af
1 <macros> 1 <macros>
2 2
3 <token name="@WRAPPER_VERSION@">1.3.2</token> 3 <token name="@WRAPPER_VERSION@">1.6.3</token>
4 4
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.3.2">r-sartools</requirement> 7 <requirement type="package" version="1.6.3">r-sartools</requirement>
8 <requirement type="package" version="1.3.2">r-optparse</requirement> 8 <requirement type="package" version="1.6.0">r-optparse</requirement>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <xml name="stdio"> 12 <xml name="stdio">
13 <stdio> 13 <stdio>
50 --report_html $report_html 50 --report_html $report_html
51 --log $log 51 --log $log
52 </token> 52 </token>
53 53
54 <macro name="basic_parameters"> 54 <macro name="basic_parameters">
55 <param name="projectName" type="text" value="Project" label="Name of the project used for the report" help="(-P, --projectName) No space allowed." > 55 <param type="text" value="Project" label="Name of the project used for the report" argument="--projectName" help="No space allowed." >
56 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 56 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
57 </param> 57 </param>
58 <param name="author" type="text" value="Galaxy" label="Name of the report author" help="(-A, --author) No space allowed." > 58 <param type="text" value="Galaxy" label="Name of the report author" argument="--author" help="No space allowed." >
59 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 59 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
60 </param> 60 </param>
61 <param name="targetFile" type="data" format="txt" label="Design / target file" help="(-t, --targetFile) See the help section below for details on the required format." /> 61 <param type="data" format="txt" label="Design / target file" argument="--targetFile" help="See the help section below for details on the required format." />
62 <param name="rawDir" type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" help="(-r, --rawDir) See the help section below for details on the required format." /> 62 <param type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" argument="--rawDir" help="See the help section below for details on the required format." />
63 <param name="featuresToRemove" type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" help="(-F, --featuresToRemove) Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." > 63 <param type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" argument="--featuresToRemove" help="Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." >
64 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 64 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
65 </param> 65 </param>
66 <param name="varInt" type="text" value="group" label="Factor of interest" help="(-v, --varInt) Biological condition in the target file. Default is 'group'." > 66 <param type="text" value="group" label="Factor of interest" argument="--varInt" help="Biological condition in the target file. Default is 'group'." >
67 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 67 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
68 </param> 68 </param>
69 <param name="condRef" type="text" value="WT" label="Reference biological condition" help="(-c, --condRef) Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." > 69 <param type="text" value="WT" label="Reference biological condition" argument="--condRef" help="Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." >
70 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 70 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
71 </param> 71 </param>
72 </macro> 72 </macro>
73 73
74 <macro name="batch_param"> 74 <macro name="batch_param">
75 <conditional name="batch_condition"> 75 <conditional name="batch_condition">
76 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="(-b, --batch) Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/> 76 <param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" argument="--batch" help="Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/>
77 <when value="NULL" /> 77 <when value="NULL" />
78 <when value="batch"> 78 <when value="batch">
79 <param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" > 79 <param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" >
80 <validator type="empty_field"/> 80 <validator type="empty_field"/>
81 </param> 81 </param>
82 </when> 82 </when>
83 </conditional> 83 </conditional>
84 </macro> 84 </macro>
85 85
86 <macro name="alpha_param"> 86 <macro name="alpha_param">
87 <param name="alpha" type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" help="(-a, --alpha) Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." /> 87 <param type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" argument="--alpha" help="Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." />
88 </macro> 88 </macro>
89 89
90 <macro name="padjustmethod_param"> 90 <macro name="padjustmethod_param">
91 <param name="pAdjustMethod" type="select" label="p-value adjustment method" help="(-p, --pAdjustMethod) p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." > 91 <param type="select" label="p-value adjustment method" argument="--pAdjustMethod" help="p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." >
92 <option value="BH" selected="true">BH</option> 92 <option value="BH" selected="true">BH</option>
93 <option value="BY">BY</option> 93 <option value="BY">BY</option>
94 <option value="bonferroni">bonferroni</option> 94 <option value="bonferroni">bonferroni</option>
95 <option value="fdr">fdr</option> 95 <option value="fdr">fdr</option>
96 <option value="hochberg">hochberg</option> 96 <option value="hochberg">hochberg</option>
98 <option value="hommel">hommel</option> 98 <option value="hommel">hommel</option>
99 </param> 99 </param>
100 </macro> 100 </macro>
101 101
102 <macro name="colors_param"> 102 <macro name="colors_param">
103 <param name="colors" type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" help="(-C, --colors) Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." > 103 <param type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" argument="--colors" help="Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." >
104 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator> 104 <validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
105 </param> 105 </param>
106 </macro>
107
108 <macro name="forceCairoGraph_param">
109 <param type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Activate cairo type" argument="--forceCairoGraph" help="Unchecked by default." />
106 </macro> 110 </macro>
107 111
108 <macro name="outputs"> 112 <macro name="outputs">
109 <data name="report_html" format="html" label="${tool.name} report" /> 113 <data name="report_html" format="html" label="${tool.name} report" />
110 <data name="tables_html" format="html" label="${tool.name} tables" /> 114 <data name="tables_html" format="html" label="${tool.name} tables" />