Mercurial > repos > bgruening > hicexplorer_hicfindtads
diff hicFindTADs.xml @ 18:d404277cc87a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 14:59:18 +0000 |
| parents | 1d9b575fe97d |
| children | 5746d61f0a91 |
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--- a/hicFindTADs.xml Fri Dec 11 21:23:33 2020 +0000 +++ b/hicFindTADs.xml Tue Mar 16 14:59:18 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin</description> <macros> <token name="@BINARY@">hicFindTADs</token> @@ -13,92 +13,83 @@ ln -s '$precomputedZscore_conditional.zscoreMatrix' 'prefix_zscore_matrix.h5' && #end if @BINARY@ - --matrix 'matrix.$matrix_h5_cooler.ext' - - --delta $delta - - #if $minBoundaryDistance: - --minBoundaryDistance $minBoundaryDistance - #end if + --matrix 'matrix.$matrix_h5_cooler.ext' + --delta $delta + #if $minBoundaryDistance: + --minBoundaryDistance $minBoundaryDistance + #end if - #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch': - --minDepth $precomputedZscore_conditional.minDepth - --maxDepth $precomputedZscore_conditional.maxDepth - --step $precomputedZscore_conditional.step - #elif $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed': - --TAD_sep_score_prefix prefix - #end if - #if $multiple_comparison_conditional.multiple_comparison_selector == 'fdr': - --correctForMultipleTesting fdr - --threshold $multiple_comparison_conditional.threshold - #elif $multiple_comparison_conditional.multiple_comparison_selector == 'bonferroni': - --correctForMultipleTesting bonferroni - --threshold $multiple_comparison_conditional.threshold - #else: - --multipleComparisons None - #end if + #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch': + --minDepth $precomputedZscore_conditional.minDepth + --maxDepth $precomputedZscore_conditional.maxDepth + --step $precomputedZscore_conditional.step + #elif $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed': + --TAD_sep_score_prefix prefix + #end if + #if $multiple_comparison_conditional.multiple_comparison_selector == 'fdr': + --correctForMultipleTesting fdr + --threshold $multiple_comparison_conditional.threshold + #elif $multiple_comparison_conditional.multiple_comparison_selector == 'bonferroni': + --correctForMultipleTesting bonferroni + --threshold $multiple_comparison_conditional.threshold + #else: + --multipleComparisons None + #end if - --numberOfProcessors @THREADS@ - --outPrefix galaxy_tad_prefix - #if $chromosomes: - --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])# - #end if - ]]></command> + --numberOfProcessors @THREADS@ + --outPrefix galaxy_tad_prefix + #if $chromosomes: + --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])# + #end if + #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch': + #if $matrix_h5_cooler.ext == 'cool': + && mv galaxy_tad_prefix*.cool matrix + #elif $matrix_h5_cooler.ext == 'h5': + && mv galaxy_tad_prefix*.h5 matrix + #end if + #end if + ]]> </command> <inputs> <expand macro='matrix_h5_cooler_macro' /> - <conditional name='precomputedZscore_conditional'> <param name='precomputedZscore_selector' type="select" label="Compute from scratch or use precomputed data"> <option value='scratch' selected='True'>From scratch</option> <option value='precomputed'>Precomputed z-score matrix</option> </param> <when value='scratch'> - - <param argument="--minDepth" type="integer" value="5000" - label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin." - help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/> - <param argument="--maxDepth" type="integer" value="10000" - label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin." - help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/> - <param argument="--step" type="integer" value="10000" - label="Step size when moving from minDepth to maxDepth" - help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...] + <param argument="--minDepth" type="integer" value="5000" label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin." help="This number should be at least 3 times as large as the bin size of the Hi-C matrix." /> + <param argument="--maxDepth" type="integer" value="10000" label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin." help="This number should around 6-10 times as large as the bin size of the Hi-C matrix." /> + <param argument="--step" type="integer" value="10000" label="Step size when moving from minDepth to maxDepth" help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...] until it reaches maxDepth. For example, selecting step=10,000, minDepth=20,000 and maxDepth=150,000 will compute TAD-scores for window sizes: - 20,000, 30,000, 40,000, 70,000 and 100,000"/> + 20,000, 30,000, 40,000, 70,000 and 100,000" /> </when> <when value='precomputed'> - <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)"/> - <param name="zscoreMatrix" type="data" format='h5' label="Precomputed z-score matrix"/> + <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)" /> + <param name="zscoreMatrix" type="data" format='cool,h5' label="Precomputed z-score matrix" /> </when> </conditional> - <conditional name="multiple_comparison_conditional"> - <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" > + <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections"> <option value="fdr" selected="True">False discovery rate</option> <option value="bonferroni">Bonferroni correction</option> <option value="None">No correction</option> </param> <when value="fdr"> - <param name="threshold" type="float" value="0.01" label="q-value" /> + <param argument="--threshold" type="float" value="0.01" label="q-value" /> </when> <when value="bonferroni"> - <param name="threshold" type="float" value="0.01" label="p-value" /> + <param argument="--threshold" type="float" value="0.01" label="p-value" /> </when> <when value="None" /> </conditional> - <param argument="--delta" type="float" value="0.001" optional="True" - label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins." - help="The delta value reduces spurious boundaries that are shallow, which usually + <param argument="--delta" type="float" value="0.001" optional="True" label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins." help="The delta value reduces spurious boundaries that are shallow, which usually occur at the center of large TADs when the TAD-sep. score is flat. Higher delta threshold values produce more conservative boundary estimations. By default, multiple delta thresholds are saved for the following delta values: 0.001, 0.01, 0.03, 0.05, 0.1. Other single or multiple values - can be given."/> - - <param argument="--minBoundaryDistance" type="integer" value="" optional="True" - label="Minimum distance between boundaries (in bp)." - help="This parameter can be used to reduce spurious boundaries caused by noise. "/> + can be given." /> + <param argument="--minBoundaryDistance" type="integer" value="" optional="True" label="Minimum distance between boundaries (in bp)." help="This parameter can be used to reduce spurious boundaries caused by noise. " /> <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0"> <param name="chromosome" type="text" label='chromosome (one per field)'> <validator type="empty_field" /> @@ -106,74 +97,80 @@ </repeat> </inputs> <outputs> - - <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed" - label="${tool.name} on ${on_string}: Boundary positions" /> - - <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph" - label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" /> - <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed" - label="${tool.name} on ${on_string}: TAD domains" /> - <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff" - format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" /> - - <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm" - format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file" > + <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed" label="${tool.name} on ${on_string}: Boundary positions" /> + <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" /> + <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed" label="${tool.name} on ${on_string}: TAD domains" /> + <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff" format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" /> + <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm" format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file"> <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter> - </data> - - <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5" - format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5"> + <data name="matrix_output" from_work_dir="matrix" format="h5" label="${tool.name} z-score matrix on ${on_string}"> <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter> + <change_format> + <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> + </change_format> </data> </outputs> <tests> <test> - <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <conditional name="precomputedZscore_conditional"> - <param name="precomputedZscore_selector" value="scratch"/> - <param name="minDepth" value="15000"/> - <param name="maxDepth" value="30000"/> - <param name="step" value="15000"/> - </conditional> - - <param name="minBoundaryDistance" value="5000" /> - <conditional name="multiple_comparison_conditional"> - <param name="multiple_comparison_selector" value="fdr"/> - <param name="threshold" value="0.8" /> - </conditional> - <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" /> - <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" /> - <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" /> - <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" /> - <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" /> - <output name="matrix_output" ftype="h5"> - <assert_contents> - <has_h5_keys keys='intervals,matrix'/> - </assert_contents> - </output> - - </test> - <test> - <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> - <conditional name="precomputedZscore_conditional"> - <param name="precomputedZscore_selector" value="precomputed"/> - <param name="scoreFile" value="find_TADs/multiFDR_tad_score.bm" /> - <param name="zscoreMatrix" value="find_TADs/multiFDR_zscore_matrix.h5"/> + <param name="precomputedZscore_selector" value="scratch" /> + <param name="minDepth" value="15000" /> + <param name="maxDepth" value="30000" /> + <param name="step" value="15000" /> </conditional> <param name="minBoundaryDistance" value="5000" /> <conditional name="multiple_comparison_conditional"> - <param name="multiple_comparison_selector" value="fdr"/> + <param name="multiple_comparison_selector" value="fdr" /> + <param name="threshold" value="0.8" /> + </conditional> + <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" /> + <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" /> + <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" /> + <output name="score" ftype="bedgraph"> + <assert_contents> + <has_n_lines n="24097" /> + <has_n_columns n="4" /> + <has_text text="chr2LHet" /> + <has_text text="chrYHet" /> + <has_text text="chrX" /> + </assert_contents> + </output> + <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" /> + <output name="matrix_output" ftype="h5"> + <assert_contents> + <has_h5_keys keys='intervals,matrix' /> + </assert_contents> + </output> + </test> + <test> + <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> + <conditional name="precomputedZscore_conditional"> + <param name="precomputedZscore_selector" value="precomputed" /> + <param name="scoreFile" value="find_TADs/multiFDR_tad_score.bm" /> + <param name="zscoreMatrix" value="find_TADs/multiFDR_zscore_matrix.h5" /> + </conditional> + <param name="minBoundaryDistance" value="5000" /> + <conditional name="multiple_comparison_conditional"> + <param name="multiple_comparison_selector" value="fdr" /> <param name="threshold" value="0.1" /> </conditional> - <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" /> - <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" /> - <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" /> - <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" /> + <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" /> + <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" /> + <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" /> + <output name="score" ftype="bedgraph"> + <assert_contents> + <has_n_lines n="24097" /> + <has_n_columns n="4" /> + <has_text text="chr2LHet" /> + <has_text text="chrYHet" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ + Calculate Topologic Associated Domains ====================================== @@ -237,6 +234,6 @@ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html .. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_ -]]></help> +]]> </help> <expand macro="citations" /> </tool>