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view carpet-src-1/tools/CARPET/calcolo_p_v4_norm.xml @ 1:78770028dcf1 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | matces |
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date | Tue, 07 Jun 2011 16:59:33 -0400 |
parents | cdd489d98766 |
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<tool id="expressions" name="TEA" version="1.0.0"> <description>Tiling Expression Analizer</description> <command interpreter="perl">calcolo_p_v4_norm_intron.pl -opt ${ann_choice.type1} -log ${ann_choice.type_data} -ann ${ann_choice.ann} -wt ${ann_choice.wt} -treat ${ann_choice.treat} -out $output -fdr ${ann_choice.fdr} -pv ${ann_choice.pv} -norm ${ann_choice.norm} -rc ${ann_choice.rc} -fc ${ann_choice.summary_choice.fc} -exon ${ann_choice.type} -sum_met ${ann_choice.summary_choice.fc_output}</command> <inputs> <conditional name="ann_choice"> <param name="type1" type="select" label="Analysis type"> <option value="comp">comparison</option> <option value="expr">expression</option> </param> <when value="comp"> <param format="tabular" name="ann" type="data" label="annotation file"/> <param format="tabular" name="wt" type="data" label="expression chip condition A"/> <param format="tabular" name="treat" type="data" label="expression chip condition B"/> <param name="type_data" type="select" label="Data type"> <option value="log">log2 value</option> <option value="no_log">raw value</option> </param> <param name="norm" type="select" label="Normalization"> <option value="yes">quantile-normalization</option> <option value="no">no normalization</option> </param> <param name="type" type="select" label="probes selection"> <option value="internal_exon">internal exon</option> <option value="all_exon">all exon</option> <option value="last_exon">last exon</option> </param> <conditional name="summary_choice"> <param name="fc_output" type="select" label="summary method"> <option value="mean">mean</option> <option value="median">median</option> <option value="both">both</option> </param> <when value="mean"> <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/> </when> <when value="median"> <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/> </when> <when value="both"> <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/> </when> </conditional> <param name="rc" size="2" type="text" value="7" label="raw value cutoff (log2)"/> <param name="fdr" type="select" label="FDR correction"> <option value="yes">yes</option> <option value="no">no</option> </param> <param name="pv" size="4" type="text" value="0.05" label="p-value cutoff"/> </when> <when value="expr"> <param format="tabular" name="ann" type="data" label="annotation file"/> <param format="tabular" name="wt" type="data" label="expression chip"/> <param format="tabular" name="treat" type="data" label="NOT NEEDED"/> <param name="type_data" type="select" label="Data type"> <option value="log">log2 value</option> <option value="no_log">raw value</option> </param> <param name="type" type="select" label="probes selection"> <option value="internal_exon">internal exon</option> <option value="all_exon">all exon</option> <option value="last_exon">last exon</option> </param> <conditional name="summary_choice"> <param name="fc_output" type="select" label="summary method"> <option value="mean">mean</option> <option value="median">median</option> <option value="both">both</option> </param> <when value="mean"> <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/> </when> <when value="median"> <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/> </when> <when value="both"> <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/> </when> </conditional> <param name="norm" size="12" type="text" value="NOT-NEEDED" label="Normalization"/> <param name="pv" size="12" type="text" value="NOT-NEEDED" label="p-value cutoff"/> <param name="fdr" size="12" type="text" value="NOT-NEEDED" label="FDR correction"/> <param name="rc" size="12" type="text" value="NOT-NEEDED" label="raw value cutoff (log2)"/> </when> </conditional> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <help> .. class:: infomark **What it does** TEA utilizes NimbleGen expression files in gff format and annotated table by ENO as INPUT FILES and generates a table with the expression value. When comparing two different conditions a Fold Change and a p-value are calculated. PLEASE, for more detailed information refer to the CARPET user Manual: click to download_ it. .. _download: /static/example_file/CARPET_userManual.zip -------- **Parameters:** - **Analysis type:** - **expression** analysis calculates an expression value for each transcript coming from the mean or the median of all matching probes - **comparison** analysis calculate an expression value for each transcript in both conditions, then calculates a Fold Change for each transcript and a p-value based on t-Test distribution. - **Data type:** - **log2 value:** the data is not converted in log2 - **raw value:** the data is converted in log2 - **Normalization:** quantile normalization between the two chips (not necessary if analysis type is "expression") - **probe selection:** - **internal exon:** only probes annotated as exons are used to calculate expression value. - **all exon:** also probes annotated at the boundaries of introns/exons are used to calculate the expression value. (probes in intronexon position usually have lower signal) - **last exon:** only probes in the last exon are used to calculate expression value. This analysis can be preferred for cDNA generated by oligo-dT RT, since 3' of transcripts are generally better represented. - **summary method:** - **mean:** fold change for each gene is calculated based on the mean value - **median:** fold change for each gene is calculated based on the median value - **both:** both are used - **Fold change cutoff:** only transcripts with FC higher than cutoff are kept - **FDR:** - **yes:** False Discovery Rate correction is applied (as described in Storie et al. 2002) - **no:** No correction --> raw p-value - **p-value cutoff:** only transcripts with p-value less than cutoff are kept - **raw value cutoff (log2):** only transcripts with raw value higher than cutoff at least in one experiment are kept -------- **INPUT FILE** Nimblegen gives you back a GFF file with the coordinates of each probe and the signal raw value. Click here_ to download a GFF file example. .. _here: /static/example_file/Expression_analysis_files.zip Example of Nimblegen Expression GFF format:: chr19 Nimblegen tiling_array 100000 1000051 20459 + . probe_name chr19 Nimblegen tiling_array 100100 1000151 1394 + . probe_name .. class:: warningmark The sixth column **must** contain the raw signal (**NOT** log2) that Nimblegen gives you back after the experiment The annotation table **MUST** be created usign ENO tool, before running TEA. --------- .. class:: infomark **How does it work?** For each gene is built the signal distibution of the probes matching Exon. -In an expression experiment, the mean or the median of the distribution represents the result of Tea. -In a comparison experiment the distibution of the gene exon signal is compared between the two conditions (1 and 2) and a t-test is performed with the possibility to introduce FDR correction. .. image:: static/images/CARPET/Tea.png **OUTPUT** - **expresion** .. image:: static/images/CARPET/expression.png - **comparison** .. image:: static/images/CARPET/comparison.png </help> </tool>