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comparison mageck_test.xml @ 1:5e2a28bee02d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
author iuc
date Sat, 17 Feb 2018 10:41:53 -0500
parents b8da4d41aa1d
children 81bbbddcf285
comparison
equal deleted inserted replaced
0:b8da4d41aa1d 1:5e2a28bee02d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mageck_test" name="MAGeCKs test" version="@VERSION@" > 2 <tool id="mageck_test" name="MAGeCKs test" version="@VERSION@.1" >
3 <description>- given a table of read counts, perform the sgRNA and gene ranking</description> 3 <description>- given a table of read counts, perform the sgRNA and gene ranking</description>
4 <macros> 4 <macros>
5 <import>mageck_macros.xml</import> 5 <import>mageck_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
29 --norm-method $adv.norm_method 29 --norm-method $adv.norm_method
30 --gene-test-fdr-threshold $adv.fdr_threshold 30 --gene-test-fdr-threshold $adv.fdr_threshold
31 --adjust-method $adv.adjust_method 31 --adjust-method $adv.adjust_method
32 $adv.var_samples 32 $adv.var_samples
33 --sort-criteria $adv.sort_criteria 33 --sort-criteria $adv.sort_criteria
34
34 --remove-zero $adv.remove_zero 35 --remove-zero $adv.remove_zero
36 #if $adv.remove_zero_threshold:
37 --remove-zero-threshold $adv.remove_zero_threshold
38 #end if
39
35 --gene-lfc-method $adv.lfc_method 40 --gene-lfc-method $adv.lfc_method
36 #if $adv.control_sgrna: 41 #if $adv.control_sgrna:
37 --control-sgrna $adv.control_sgrna 42 --control-sgrna $adv.control_sgrna
38 #end if 43 #end if
44
39 #if $adv.cnv_norm: 45 #if $adv.cnv_norm:
40 --cnv-norm $adv.cnv_norm 46 --cnv-norm $adv.cnv_norm
41 #end if 47 #end if
48
42 #if $adv.cell_line: 49 #if $adv.cell_line:
43 --cell-line $adv.cell_line 50 --cell-line $adv.cell_line
44 #end if 51 #end if
45 52
46 ]]></command> 53 ]]></command>
63 70
64 <section name="out" title="Output Options"> 71 <section name="out" title="Output Options">
65 <param name="normcounts" argument="--normcounts-to-file" type="boolean" truevalue="--normcounts-to-file" falsevalue="" checked="false" optional="true" label="Output normalized counts file" help="Default: No" /> 72 <param name="normcounts" argument="--normcounts-to-file" type="boolean" truevalue="--normcounts-to-file" falsevalue="" checked="false" optional="true" label="Output normalized counts file" help="Default: No" />
66 <param name="pdfreport" argument="--pdf-report" type="boolean" truevalue="--pdf-report" falsevalue="" checked="false" optional="true" label="Output PDF report" help="Generate pdf report of the input file. Default: No" /> 73 <param name="pdfreport" argument="--pdf-report" type="boolean" truevalue="--pdf-report" falsevalue="" checked="false" optional="true" label="Output PDF report" help="Generate pdf report of the input file. Default: No" />
67 <param name="rscriptOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output R script" help="Output the R script used to generate the plots in the pdf report. Default: No" /> 74 <param name="rscriptOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output R script" help="Output the R script used to generate the plots in the pdf report. Default: No" />
68 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output logfile" help="This file includes the logging information during the execution. Default: No" /> 75 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output Log file" help="This file includes the logging information during the execution. Default: No" />
69 </section> 76 </section>
70 77
71 <section name="adv" title="Advanced Options"> 78 <section name="adv" title="Advanced Options">
72 <param name="norm_method" argument="--norm-method" type="select" label="Method for normalization" 79 <param name="norm_method" argument="--norm-method" type="select" label="Method for normalization"
73 help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" > 80 help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" >
82 <option value="holm">Holm</option> 89 <option value="holm">Holm</option>
83 <option value="pounds">Pounds</option> 90 <option value="pounds">Pounds</option>
84 </param> 91 </param>
85 <param name="var_samples" argument="--variance-from-all-samples" type="boolean" truevalue="--variance-from-all-samples" falsevalue="" checked="false" optional="true" label="Estimate the variance from all samples, instead of from only control samples" help="Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples" /> 92 <param name="var_samples" argument="--variance-from-all-samples" type="boolean" truevalue="--variance-from-all-samples" falsevalue="" checked="false" optional="true" label="Estimate the variance from all samples, instead of from only control samples" help="Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples" />
86 <expand macro="sort_criteria" /> 93 <expand macro="sort_criteria" />
87 <param name="remove_zero" argument="--remove-zero" type="select" help="Whether to remove zero-count sgRNAs in control and/or treatment experiments {none,control,treatment,both}. Default: None (do not remove those zero-count sgRNAs)" > 94 <param name="remove_zero" argument="--remove-zero" type="select" label="Remove zero" help="Remove sgRNAs whose mean value is zero in Control, Treatment, Both control/treatment, or Any control/treatment sample. Default: Both (remove those sgRNAs that are zero in both control and treatment samples)" >
88 <option value="none" selected="True">None</option> 95 <option value="none" >None</option>
89 <option value="control">Control</option> 96 <option value="control">Control</option>
90 <option value="treatment">Treatment</option> 97 <option value="treatment">Treatment</option>
91 <option value="both">Both</option> 98 <option value="both" selected="True">Both</option>
92 </param> 99 <option value="any">Any</option>
100 </param>
101 <param name="remove_zero_threshold" argument="--remove-zero-threshold" type="float" value="0" label="Remove zero Threshold" help="sgRNA normalized count threshold to be considered removed in the --remove-zero option. Default: 0"/>
93 <param name="lfc_method" argument="--gene-lfc-method" type="select" label="Gene Log-Fold Change Method." help="Method to calculate gene log fold changes (LFC) from sgRNA LFCs. Available methods include the median/mean of all sgRNAs (median/mean), or the median/mean sgRNAs that are ranked in front of the alpha cutoff in RRA (alphamedian/alphamean), or the sgRNA that has the second strongest LFC (secondbest). In the alphamedian/alphamean case, the number of sgRNAs correspond to the goodsgrna column in the output, and the gene LFC will be set to 0 if no sgRNA is in front of the alpha cutoff. Default: Median. (new since v0.5.5)"> 102 <param name="lfc_method" argument="--gene-lfc-method" type="select" label="Gene Log-Fold Change Method." help="Method to calculate gene log fold changes (LFC) from sgRNA LFCs. Available methods include the median/mean of all sgRNAs (median/mean), or the median/mean sgRNAs that are ranked in front of the alpha cutoff in RRA (alphamedian/alphamean), or the sgRNA that has the second strongest LFC (secondbest). In the alphamedian/alphamean case, the number of sgRNAs correspond to the goodsgrna column in the output, and the gene LFC will be set to 0 if no sgRNA is in front of the alpha cutoff. Default: Median. (new since v0.5.5)">
94 <option value="median" selected="True">Median</option> 103 <option value="median" selected="True">Median</option>
95 <option value="alphamedian">Alphamedian</option> 104 <option value="alphamedian">Alphamedian</option>
96 <option value="mean">Mean</option> 105 <option value="mean">Mean</option>
97 <option value="alphamean">Alphamean</option> 106 <option value="alphamean">Alphamean</option>