Mercurial > repos > bgruening > diffbind
diff 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 |
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--- a/diffbind.xml Thu Apr 19 17:15:53 2018 -0400 +++ b/diffbind.xml Wed May 30 12:25:42 2018 -0400 @@ -1,4 +1,4 @@ -<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> @@ -106,7 +106,7 @@ <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> @@ -133,9 +133,9 @@ <!-- 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="wig">WIG</option> + <option value="tabular">Tabular (tab-separated)</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" /> @@ -146,7 +146,12 @@ </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> @@ -165,34 +170,72 @@ </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="analysis_info" value="out_analysis_info.txt" compare="sim_size" > + <output name="rscript"> + <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[ @@ -283,7 +326,7 @@ 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 @@ -295,42 +338,72 @@ **Differentially Bound Sites** -Example: +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**: - ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ======== - 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 - ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ======== + ====== ====== ====== ======== ===== ====== =========================================== + 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: -* **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 +* **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. +differential analysis. Note that this output is a tabular 0-based format. 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 @@ -426,6 +499,8 @@ .. _`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>