diffbind: diffbind.xml comparison

comparison diffbind.xml @ 13:1de83981d43c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610

author	iuc
date	Wed, 30 May 2018 12:25:42 -0400
parents	fa56d93f7980
children	c97a786e8fb5

comparison

equal deleted inserted replaced

-:fa56d93f7980
+:1de83981d43c
-<tool id="diffbind" name="DiffBind" version="2.6.6.2">
+<tool id="diffbind" name="DiffBind" version="2.6.6.3">
 <description> differential binding analysis of ChIP-Seq peak data</description>
 <requirements>
 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
 <requirement type="package" version="1.20.0">r-getopt</requirement>
 <requirement type="package" version="0.2.15">r-rjson</requirement>
 ]]>
 </command>
 <inputs>
 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
 <param name="groupName" type="text" label="Name"
-help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
+help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
 <sanitizer>
 <valid initial="string.letters,string.digits"><add value="_" /></valid>
 </sanitizer>
 <validator type="empty_field" />
 </param>
 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/>
 <!-- Output Options -->
 <section name="out" expanded="false" title="Output Options">
 <param name="format" type="select" label="Output Format">
+<option value="interval" selected="True">Interval</option>
 <option value="bed">BED</option>
-<option value="gff">GFF</option>
+<option value="tabular">Tabular (tab-separated)</option>
-<option value="wig">WIG</option>
 </param>
 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" />
 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />
 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/>
 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/>
 </section>
 </inputs>
 <outputs>
-<data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Differentially bound sites" />
+<data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites">
+<change_format>
+<when input="out.format" value="bed" format="bed" />
+<when input="out.format" value="tabular" format="tabular" />
+</change_format>
+</data>
 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
 <filter>out['pdf']</filter>
 </data>
 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
 <filter>out['binding_matrix']</filter>
 <filter>out['analysis_info']</filter>
 </data>
 </outputs>
 <tests>
+<!-- Ensure outputs work -->
 <test expect_num_outputs="6">
 <repeat name="rep_group">
 <param name="groupName" value="Resistant"/>
-<param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
+<param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
 </repeat>
 <repeat name="rep_group">
 <param name="groupName" value="Responsive"/>
-<param name="peaks" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
+<param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
 </repeat>
 <param name="scorecol" value="5" />
+<param name="format" value="interval"/>
 <param name="pdf" value="True" />
 <param name="binding_matrix" value="True" />
 <param name="rdata" value="True" />
 <param name="rscript" value="True"/>
 <param name="analysis_info" value="True"/>
-<output name="outfile" value="out_diffbind.tab" />
+<output name="outfile" ftype="interval" value="out_diffbind.interval" />
 <output name="plots" value="out_plots.pdf" compare="sim_size" />
-<output name="binding_matrix" value="out_binding.matrix" />
+<output name="binding_matrix" value="out_binding_matrix.tab" />
 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
-<output name="rscript" value="out_rscript.txt"/>
+<output name="rscript">
-<output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" >
+<assert_contents>
+<has_text text="write.table"/>
+</assert_contents>
+</output>
+<output name="analysis_info" compare="sim_size" >
 <assert_contents>
 <has_text text="SessionInfo"/>
 </assert_contents>
 </output>
+</test>
+<!-- Ensure BED output works -->
+<test expect_num_outputs="1">
+<repeat name="rep_group">
+<param name="groupName" value="Resistant"/>
+<param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
+<param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
+</repeat>
+<repeat name="rep_group">
+<param name="groupName" value="Responsive"/>
+<param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
+<param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
+</repeat>
+<param name="scorecol" value="5" />
+<param name="format" value="bed"/>
+<output name="outfile" ftype="bed" value="out_diffbind.bed" />
+</test>
+<!-- Ensure tabular output works -->
+<test expect_num_outputs="1">
+<repeat name="rep_group">
+<param name="groupName" value="Resistant"/>
+<param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
+<param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
+</repeat>
+<repeat name="rep_group">
+<param name="groupName" value="Responsive"/>
+<param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
+<param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
+</repeat>
+<param name="scorecol" value="5" />
+<param name="format" value="tabular"/>
+<output name="outfile" ftype="tabular" file="out_diffbind.tab" />
 </test>
 </tests>
 <help><![CDATA[
 .. class:: infomark
 **Outputs**
 This tool outputs
-* a table of differentially bound sites
+* a table of differentially bound sites in Interval, BED or Tabular 0-based format
 Optionally, under **Output Options** you can choose to output
 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
 * a binding affinity matrix
 * an RData file of the R objects generated
 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
 **Differentially Bound Sites**
+The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_.
+Example - **Interval format**:
+======  ======  ======  ========  =====  ======  ===========================================
+Chrom   Start   End     Name      Score  Strand  **Comment**
+======  ======  ======  ========  =====  ======  ===========================================
+chr18   394599  396513  DiffBind    0      \.    1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21
+chr18   111566  112005  DiffBind    0      \.    439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06
+chr18   346463  347342  DiffBind    0      \.    879|5|5.77|3.24|2.52|6.51e-06|0.00303
+chr18   399013  400382  DiffBind    0      \.    1369|7.62|7|8.05|-1.04|1.04e-05|0.00364
+chr18   371109  372102  DiffBind    0      \.    993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226
+======  ======  ======  ========  =====  ======  ===========================================
+Columns contain the following data:
+* **Chrom**: Chromosome name
+* **Start**: Start position of site
+* **End**: End position of site
+* **Score**: 0
+* **Name**: DiffBind
+* **Strand**: Strand
+* **Comment**: The pipe ("|") separated values in this column correspond to:
+* *width*: Length of site
+* *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
+* *Conc_Group1*: Mean concentration over the first group (e.g. Responsive)
+* *Conc_Group2*: Mean concentration over second group (e.g. Resistant)
+* *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
+* *p.value*: P-value confidence measure for identifying these sites as differentially bound
+* *FDR*: a multiple testing corrected FDR p-value
+Example - **BED format**:
+=====  ======  ======  ========  =====  ======
+Chrom  Start   End     Name      Score  Strand
+=====  ======  ======  ========  =====  ======
+chr18  394599  396513  DiffBind    0      \.
+chr18  111566  112005  DiffBind    0      \.
+chr18  346463  347342  DiffBind    0      \.
+chr18  399013  400382  DiffBind    0      \.
+chr18  371109  372102  DiffBind    0      \.
+=====  ======  ======  ========  =====  ======
+Example - **Tabular format**:
+=====  ======  ======  ========  =====  ======  ====  ===============  ==============  =====  ========  ========
+Chrom  Start   End     Name      Score  Strand  Conc  Conc_Responsive  Conc_Resistant  Fold   p.value   FDR
+=====  ======  ======  ========  =====  ======  ====  ===============  ==============  =====  ========  ========
+chr18  394599  396513  DiffBind    0      \.    7.15  5.55             7.89            -2.35  7.06E-24  9.84E-21
+chr18  111566  112005  DiffBind    0      \.    5.71  6.53             3.63            2.89   1.27E-08  8.88E-06
+chr18  346463  347342  DiffBind    0      \.    5     5.77             3.24            2.52   6.51E-06  0.00303
+chr18  399013  400382  DiffBind    0      \.    7.62  7                8.05            -1.04  1.04E-05  0.00364
+chr18  371109  372102  DiffBind    0      \.    4.63  3.07             5.36            -2.3   8.10E-05  0.0226
+=====  ======  ======  ========  =====  ======  ====  ===============  ==============  =====  ========  ========
+**Binding Affinity Matrix**
+The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
+differential analysis. Note that this output is a tabular 0-based format.
 Example:
-========  ======  ======  =====  ======  =====  ===============  ==============  ======  ========  ========
-seqnames  start   end     width  strand  Conc   Conc_Responsive  Conc_Resistant  Fold    p.value   **FDR**
-========  ======  ======  =====  ======  =====  ===============  ==============  ======  ========  ========
-chr18     394600  396513  1914    \*     7.15   5.55             7.89            -2.35   7.06e-24  9.84e-21
-chr18     111567  112005  439     \*     5.71   6.53             3.63            2.89    1.27e-08  8.88e-06
-chr18     346464  347342  879     \*     5      5.77             3.24            2.52    6.51e-06  0.00303
-chr18     399014  400382  1369    \*     7.62   7                8.05            -1.04   1.04e-05  0.00364
-chr18     371110  372102  993     \*     4.63   3.07             5.36            -2.3    8.1e-05   0.0226
-========  ======  ======  =====  ======  =====  ===============  ==============  ======  ========  ========
-Columns contain the following data:
-* **seqnames**: Chromosome name
-* **start**: Start position of site
-* **end**: End position of site
-* **width**: Length of site
-* **strand**: Strand
-* **Conc**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
-* **Responsive**: Mean concentration over the first (e.g. Responsive) group
-* **Resistant**: Mean concentration over second (e.g. Resistant) group
-* **Fold**: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
-* **p.value**: P-value confidence measure for identifying these sites as differentially bound
-* **FDR**: a multiple testing corrected FDR p-value
-**Binding Affinity Matrix**
-The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
-differential analysis.
-Example:
 =====  ======  ======  =========  =========  ==========  ==========
-CHR    START   END     MCF7_ER_1  MCF7_ER_2  BT474_ER_1  BT474_ER_2
+Chrom  Start   End     MCF7_ER_1  MCF7_ER_2  BT474_ER_1  BT474_ER_2
 =====  ======  ======  =========  =========  ==========  ==========
 chr18  111567  112005  137.6152   59.87837   29.41393    19.95945
 chr18  189223  189652  19.95945   12.60597   11.55547    23.11095
 chr18  215232  216063  11.55547   15.75746   31.51493    72.48434
 chr18  311530  312172  17.85846   11.55547   54.62588    43.07040
 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
+.. _here: https://galaxyproject.org/learn/datatypes/#interval
+.. _`Biostars post`: https://www.biostars.org/p/84686/
 ]]>
 </help>
 <citations>
 <citation type="doi">doi:10.1038/nature10730</citation>

Mercurial > repos > bgruening > diffbind

comparison diffbind.xml @ 13:1de83981d43c draft