diff minfi_TCGA_pipeline.xml @ 0:8b26eeb2da29 draft

planemo upload commit fb90aafc93e5e63acfcdac4c27cfd865cdf06c5a-dirty

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+++ b/minfi_TCGA_pipeline.xml	Tue Apr 19 11:11:16 2016 -0400
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+<tool id="minfi_analyze_tcga" name="Minfi Analysis Pipeline" version="1.0">
+    <description>for TCGA data hosted on GDAC-Broadinstitute</description>
+    <macros>
+        <import>minfi_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir tcga_temp
+        &&
+        echo "${tarfile},${tarfile.name}" > tcga_temp/config.txt
+        &&
+        Rscript ${__tool_directory__}/minfi_TCGA_pipeline.R
+        --quiet="FALSE"
+        --tarfile="${tarfile}"
+        --cores=\${GALAXY_SLOTS:-4}
+        #if str( $minfi_param_type.minfi_param_type_selector ) == "advanced":
+            --b_permutations=${minfi_param_type.b_permutations}
+            --smooth=${minfi_param_type.smooth}
+            --l_value=${minfi_param_type.l_value}
+        #else:
+            --b_permutations=25
+            --smooth=FALSE
+            --l_value=4
+        #end if
+        ]]> </command>
+    <inputs>
+        <param name="tarfile" type="data" label="Input GDAC filename"/>
+        <conditional name="minfi_param_type">
+            <param name="minfi_param_type_selector" type="select" label="Basic or Advanced Minfi Parameters">
+                <option value="basic" selected="True">Basic Default settings</option>
+                <option value="advanced">Advanced</option>
+            </param>
+            <when value="basic">
+                <!--Do nothing here -->
+            </when>
+            <when value="advanced">
+                <!-- Give options for estimating cell counts here -->
+                <!-- Give Bumphunter options here like B,smooth,cutoff, length of dmrs-->
+                <param name="b_permutations" type="integer" value="25" label="Number of times resampled" help="Refer the tool's help section" />
+                <param name="smooth" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Should a smoothing function be used?" help="Refer the tool's help section" />
+                <param name="l_value" type="integer" value="4" label="Length of DMRs to be selected" help="Refer the tool's help section" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <!-- PLOT OUTPUTS -->
+        <!-- CSV outputs -->
+        <data name="dmps" from_work_dir="dmps.csv" format="csv" label="Differentially Methylated positions" />
+        <data name="dmrs" from_work_dir="dmrs.csv" format="csv" label="Differentially Methylated Regions using Bumphunter" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="tarfile" value="gdac.broadinstitute.org_UCEC.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2014101700.0.0.tar" />
+            <param name="minfi_param_type.minfi_param_type_selector" value="basic" />
+            <output name="dmps_tcga" file="dmps_tcga.csv" ftype="csv" />
+            <output name="dmrs_tcga" file="dmrs_tcga.csv" ftype="csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Analyze TCGA illumina 450k array data hosted at the GDAC Broadinstitute firehose.
+http://gdac.broadinstitute.org/runs/stddata__latest/
+
+**Input**:
+
+Currently, an example of a file that this function reads is here:
+
+<http://gdac.broadinstitute.org/runs/stddata__2014_10_17/data/UCEC/20141017/gdac.broadinstitute.org_UCEC.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2014101700.0.0.tar.gz>
+
+
+NOTE: It is an archive of size 8.1Gb
+
+1. Upload the file into galaxy.
+
+2. Run the "Minfi Analysis pipeline for TCGA data" tool on the resultant tar file in your history.
+
+3. This will generate two results, Differentially methylated positions and Differentially methylated regions.
+
+**Output**:
+
+1. Differentially methylated positions
+
+2. Differentially methylated regions.
+
+]]></help>
+    <expand macro="citations" />
+</tool>
+