comparison sleuth.xml @ 3:2c3d294dbe42 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 4adb19064a6973121680119529444286c24c1ac1

2:d6b5fc94062c

<tool id="sleuth" name="Sleuth" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
    <description>differential expression analysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro='requirements'/>
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator." />
        <regex match="Fatal error"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator." />
    </stdio>
    <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command>
    <command><![CDATA[
        #import os
        mkdir -p './kallisto_outputs' &&

            <when value="single">
                <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
                    <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
                        help="Only letters, numbers and underscores will be retained in this field">
                        <sanitizer>
                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
                        </sanitizer>
                    </param>
                    <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
                </repeat>
            </when>
            <when value="complex">
                <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section." />
            </when>
        </conditional>
        <section name="advanced_options" title="Advanced options" expanded="true">
            <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" 
                help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should 
                    only be set to false if one desires to do a quick check of the raw data. " />
            <param argument="nbins" type="integer" min="0" value="100" label="NBins" help="The number of bins that the data should be 
                split for the sliding window shrinkage using the mean-variance curve." />
            <param argument="lwr" type="float" min="0" max="1" value="0.25" label="LWR" help="The lower range of variances within each 
                bin that should be included for the shrinkage procedure. " />
            <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each 
                bin that should be included for the shrinkage procedure." />
        </section>

    </inputs>
    <outputs>
        <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
            <actions>
                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq" />
            </actions>
        </data>
        <data name="pca_plot" from_work_dir="pca_plot.pdf" format="pdf" label="${tool.name} on ${on_string}: PCA plot"/>
        <data name="density_plot" from_work_dir="group_density.pdf" format="pdf" label="${tool.name} on ${on_string}: density plot"/>
    </outputs>

                <param name="lwr" value="0.25"/>
                <param name="upr" value="0.75"/>
            </section>
            <output name="sleuth_table" ftype="tabular">
                <assert_contents>
                    <has_size value="756310" delta="100"/>
                    <has_text text="ENST00000394894.8"/>
                    <has_text text="ENST00000524187.1"/>
                </assert_contents>
            </output>
            <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/>

                <param name="lwr" value="0.25"/>
                <param name="upr" value="0.75"/>
            </section>
            <output name="sleuth_table" ftype="tabular">
                <assert_contents>
                    <has_size value="756310" delta="100"/>
                    <has_text text="ENST00000394894.8"/>
                    <has_text text="ENST00000524187.1"/>
                </assert_contents>
            </output>
            <output name="pca_plot" file="test03_pca.pdf" ftype="pdf" compare="sim_size"/>

The tabular file **requires to have at least three columns with the same names as the previous example** (path, condition, sample). The path column correspond to original FASTQ filenames uploaded to Galaxy. 
Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. 
Additional factors can be included in the design table.

    ]]></help>
    <expand macro="citations" />
</tool>

3:2c3d294dbe42

<tool id="sleuth" name="Sleuth" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
    <description>Differential expression analysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro='requirements'/>
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted."/>
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
        <regex match="Fatal error"
           source="both"
           level="fatal"
           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
    </stdio>
    <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command>
    <command><![CDATA[
        #import os
        mkdir -p './kallisto_outputs' &&

            <when value="single">
                <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
                    <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
                        help="Only letters, numbers and underscores will be retained in this field">
                        <sanitizer>
                            <valid initial="string.letters,string.digits"><add value="_"/></valid>
                        </sanitizer>
                    </param>
                    <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
                </repeat>
            </when>
            <when value="complex">
                <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section."/>
            </when>
        </conditional>
        <section name="advanced_options" title="Advanced options" expanded="true">
            <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" 
                help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should 
                    only be set to false if one desires to do a quick check of the raw data. "/>
            <param argument="nbins" type="integer" min="0" value="100" label="NBins" help="The number of bins that the data should be 
                split for the sliding window shrinkage using the mean-variance curve."/>
            <param argument="lwr" type="float" min="0" max="1" value="0.25" label="LWR" help="The lower range of variances within each 
                bin that should be included for the shrinkage procedure. "/>
            <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each 
                bin that should be included for the shrinkage procedure."/>
        </section>

    </inputs>
    <outputs>
        <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
            <actions>
                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq"/>
            </actions>
        </data>
        <data name="pca_plot" from_work_dir="pca_plot.pdf" format="pdf" label="${tool.name} on ${on_string}: PCA plot"/>
        <data name="density_plot" from_work_dir="group_density.pdf" format="pdf" label="${tool.name} on ${on_string}: density plot"/>
    </outputs>

                <param name="lwr" value="0.25"/>
                <param name="upr" value="0.75"/>
            </section>
            <output name="sleuth_table" ftype="tabular">
                <assert_contents>
                    <has_size value="756425" delta="100"/>
                    <has_text text="ENST00000394894.8"/>
                    <has_text text="ENST00000524187.1"/>
                </assert_contents>
            </output>
            <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/>

                <param name="lwr" value="0.25"/>
                <param name="upr" value="0.75"/>
            </section>
            <output name="sleuth_table" ftype="tabular">
                <assert_contents>
                    <has_size value="756425" delta="100"/>
                    <has_text text="ENST00000394894.8"/>
                    <has_text text="ENST00000524187.1"/>
                </assert_contents>
            </output>
            <output name="pca_plot" file="test03_pca.pdf" ftype="pdf" compare="sim_size"/>

The tabular file **requires to have at least three columns with the same names as the previous example** (path, condition, sample). The path column correspond to original FASTQ filenames uploaded to Galaxy. 
Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. 
Additional factors can be included in the design table.

    ]]></help>
    <expand macro="citations"/>
</tool>