comparison mageck_test.xml @ 1:5e2a28bee02d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7

0:b8da4d41aa1d

<?xml version="1.0"?>
<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@" >
    <description>- given a table of read counts, perform the sgRNA and gene ranking</description>
    <macros>
        <import>mageck_macros.xml</import>
    </macros>
    <expand macro="requirements" />

--norm-method $adv.norm_method
--gene-test-fdr-threshold $adv.fdr_threshold
--adjust-method $adv.adjust_method
$adv.var_samples
--sort-criteria $adv.sort_criteria
--remove-zero $adv.remove_zero
--gene-lfc-method $adv.lfc_method
#if $adv.control_sgrna:
    --control-sgrna $adv.control_sgrna
#end if
#if $adv.cnv_norm:
    --cnv-norm $adv.cnv_norm
#end if
#if $adv.cell_line:
    --cell-line $adv.cell_line
#end if

    ]]></command>

        <section name="out" title="Output Options">
            <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"  />
            <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" />
            <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" />
            <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" />
        </section>

        <section name="adv" title="Advanced Options">
            <param name="norm_method" argument="--norm-method" type="select" label="Method for normalization"
                help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" >

            <option value="holm">Holm</option>
            <option value="pounds">Pounds</option>
        </param>
        <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" />
        <expand macro="sort_criteria" />
        <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)" >
            <option value="none" selected="True">None</option>
            <option value="control">Control</option>
            <option value="treatment">Treatment</option>
            <option value="both">Both</option>
        </param>
        <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)">
            <option value="median" selected="True">Median</option>
            <option value="alphamedian">Alphamedian</option>
            <option value="mean">Mean</option>
            <option value="alphamean">Alphamean</option>

1:5e2a28bee02d

<?xml version="1.0"?>
<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@.1" >
    <description>- given a table of read counts, perform the sgRNA and gene ranking</description>
    <macros>
        <import>mageck_macros.xml</import>
    </macros>
    <expand macro="requirements" />

--norm-method $adv.norm_method
--gene-test-fdr-threshold $adv.fdr_threshold
--adjust-method $adv.adjust_method
$adv.var_samples
--sort-criteria $adv.sort_criteria

--remove-zero $adv.remove_zero
#if $adv.remove_zero_threshold:
    --remove-zero-threshold $adv.remove_zero_threshold
#end if

--gene-lfc-method $adv.lfc_method
#if $adv.control_sgrna:
    --control-sgrna $adv.control_sgrna
#end if

#if $adv.cnv_norm:
    --cnv-norm $adv.cnv_norm
#end if

#if $adv.cell_line:
    --cell-line $adv.cell_line
#end if

    ]]></command>

        <section name="out" title="Output Options">
            <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"  />
            <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" />
            <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" />
            <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" />
        </section>

        <section name="adv" title="Advanced Options">
            <param name="norm_method" argument="--norm-method" type="select" label="Method for normalization"
                help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" >

            <option value="holm">Holm</option>
            <option value="pounds">Pounds</option>
        </param>
        <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" />
        <expand macro="sort_criteria" />
        <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)" >
            <option value="none" >None</option>
            <option value="control">Control</option>
            <option value="treatment">Treatment</option>
            <option value="both" selected="True">Both</option>
            <option value="any">Any</option>
        </param>
        <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"/>
        <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)">
            <option value="median" selected="True">Median</option>
            <option value="alphamedian">Alphamedian</option>
            <option value="mean">Mean</option>
            <option value="alphamean">Alphamean</option>