| Previous changeset 1:7e0a12282c7f (2017-03-28) |
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Commit message:
"planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" |
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modified:
macros.xml multigps.xml test-data/hg19_all_events_table1.tabular test-data/hg19_all_events_table2.tabular test-data/hg19_output_html1.html test-data/hg19_output_html2.html test-data/hg19_replicates_counts1.tabular test-data/hg19_replicates_counts2.tabular |
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added:
test-data/hg19_output_bed1.bed test-data/hg19_output_bed2.bed tool-data/hg19.len |
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removed:
.shed.yml |
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| diff -r 7e0a12282c7f -r 028fafca04fa .shed.yml --- a/.shed.yml Tue Mar 28 12:24:56 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -name: multigps -owner: iuc -description: Analyzes collections of multi-condition ChIP-seq data. -homepage_url: http://mahonylab.org/software/multigps/ -long_description: | - Contains a tool that runs MultiGPS, a framework for analyzing collections of multi-condition ChIP-seq - datasets and characterizing differential binding events between conditions. MultiGPS encourages consistency - in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment - levels at each event. MultiGPS loads all data to memory, so you will need a lot of available memory if you - are running analysis over many conditions or large datasets. -type: unrestricted -categories: -- ChIP-seq |
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| diff -r 7e0a12282c7f -r 028fafca04fa macros.xml --- a/macros.xml Tue Mar 28 12:24:56 2017 -0400 +++ b/macros.xml Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,8 +1,33 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> + <xml name="cond_fixedreadcount"> + <conditional name="fixedreadcount_cond"> + <param name="fixedreadcount_select" type="select" label="Set fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="fixedreadcount" type="integer" value="0" min="0" label="Fixed per-base read count limit"/> + </when> + </conditional> + </xml> + <xml name="param_experiment_type"> + <param name="experiment_type" type="select" display="radio" label="Experiment type for this replicate"> + <option value="chipseq" selected="True">ChIP-seq</option> + <option value="chipexo">ChIP-exo</option> + </param> + </xml> <xml name="motif_finding_params"> <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" /> <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" /> <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" /> </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1">fonts-conda-ecosystem</requirement> + <requirement type="package" version="0.74">multigps</requirement> + <yield/> + </requirements> + </xml> </macros> |
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| diff -r 7e0a12282c7f -r 028fafca04fa multigps.xml --- a/multigps.xml Tue Mar 28 12:24:56 2017 -0400 +++ b/multigps.xml Sun Dec 22 12:11:33 2019 -0500 |
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| b'@@ -1,31 +1,28 @@\n-<tool id="multigps" name="MultiGPS" version="0.73.0">\n+<tool id="multigps" name="MultiGPS" version="0.74.0">\n <description>analyzes collections of multi-condition ChIP-seq data</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="0.73">multigps</requirement>\n- </requirements>\n+ <expand macro="requirements" />\n <command detect_errors="aggressive">\n <![CDATA[\n #set output_dir = $output_html.files_path\n mkdir -p $output_dir &&\n multigps\n ## General options\n+ --design \'$build_design_file\'\n ## Append .txt extensions to events hrefs\n ## in output dataset so files will render\n ## in the browser.\n --eventsaretxt\n- ## Do not run the parallel version of meme\n- ## since it is not yet available in conda.\n+ ## Do not run the parallel version of meme.\n --meme1proc\n- --expt \'$expt\'\n- --format $expt.ext\n- #if str($ctrl) != \'None\':\n- --ctrl \'$ctrl\'\n+ --threads \\${GALAXY_SLOTS:-4}\n+ #if str($in_test_mode) == "no":\n+ --geninfo \'$chromInfo\'\n+ #else:\n+ --geninfo \'$__tool_directory__/tool-data/hg19.len\'\n #end if\n- --threads \\${GALAXY_SLOTS:-4}\n- --geninfo \'$chromInfo\'\n ## Advanced options\n #set aoc = $advanced_options_cond\n #if str($aoc.advanced_options) == \'display\':\n@@ -39,9 +36,9 @@\n #set rgc = $umc.reference_genome_cond\n --seq\n #if str($rgc.reference_genome_source) == \'cached\':\n-\t\t \'${rgc.reference_genome.fields.path}\'\n+ \'${rgc.reference_genome.fields.path}\'\n #else:\n-\t\t \'${rgc.reference_genome}\'\n+ \'${rgc.reference_genome}\'\n #end if\n #end if\n ## Limits on how many reads\n@@ -80,9 +77,9 @@\n #end if\n ## Running MultiGPS\n #if str($aoc.readdistributionfile) != \'None\':\n- --d \'$aoc.readdistributionfile\'\n+ --readdistributionfile \'$aoc.readdistributionfile\'\n #end if\n- --r $aoc.maxtrainingrounds\n+ --maxtrainingrounds $aoc.maxtrainingrounds\n #if str($aoc.nomodelupdate) == \'no\':\n --nomodelupdate\n #end if\n@@ -127,20 +124,20 @@\n --mememinw $bmc.mememinw\n --mememaxw $bmc.mememaxw\n #else:\n- #set mfoc = $bmc.nomotifprior_cond\n+ #set nmpc = $bmc.nomotifprior_cond\n --nomotifs\n- --nomotifprior $mfoc.nomotifprior\n- #if str($mfoc.nomotifprior) == \'yes\':\n- --memenmotifs $mfoc.memenmotifs\n- --mememinw $mfoc.mememinw\n- --mememaxw $mfoc.mememaxw\n+ #if str($nmpc.nomotifprior) == \'yes\':\n+ --nomotifprior\n+ --memenmotifs $nmpc.memenmotifs\n+ --mememinw $nmpc.mememinw\n+ --mememaxw $nmpc.mememaxw\n #end if\n #end if\n #end if\n #end if\n ## Reporting binding events\n #if str($rbec.report_binding_events) == \'yes\':\n- --q $rbec.minqvalue\n+ --minqvalue $rbec.minqvalue\n --minfold $rbec.minfold\n #if str($rbec.nodifft'..b'rmat="tabular" label="${tool.name} replicates counts on ${on_string}"/>\n- <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/>\n- <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/>\n- <data name="output_html" format="html" label="${tool.name} on ${on_string}"/>\n+ <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">\n+ <filter>save_design_file == \'yes\'</filter>\n+ </data>\n+ <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>\n+ <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>\n+ <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>\n+ <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>\n </outputs>\n <tests>\n <test>\n- <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />\n- <param name="advanced_options_cond" value="hide" />\n+ <repeat name="condition_repeat">\n+ <repeat name="signal_repeat">\n+ <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />\n+ </repeat>\n+ </repeat>\n+ <param name="advanced_options" value="hide" />\n+ <param name="in_test_mode" value="yes" />\n <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>\n- <output name="experiment_events" file="hg19_experiment_events1.tabular" ftype="tabular"/>\n+ <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>\n <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>\n <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>\n </test>\n <test>\n- <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />\n- <param name="ctrl" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />\n- <param name="advanced_options_cond" value="display" />\n+ <repeat name="condition_repeat">\n+ <repeat name="signal_repeat">\n+ <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />\n+ </repeat>\n+ <repeat name="control_repeat">\n+ <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />\n+ </repeat>\n+ </repeat>\n+ <param name="advanced_options" value="display" />\n+ <param name="in_test_mode" value="yes" />\n <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>\n- <output name="experiment_events" file="hg19_experiment_events2.tabular" ftype="tabular"/>\n+ <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>\n <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>\n <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>\n </test>\n@@ -399,7 +472,7 @@\n \n * **Loading data:**\n \n- - **Optional file containing reads from a control experiment** - must be same format as input experiment\n+ - **Optional file containing reads from a control experiment** - file containing reads from a control experiment\n - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).\n - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.\n - **Use non-unique reads** - Use non-unique reads.\n@@ -456,3 +529,4 @@\n <citation type="doi">10.1371/journal.pcbi.1003501</citation>\n </citations>\n </tool>\n+\n' |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_all_events_table1.tabular --- a/test-data/hg19_all_events_table1.tabular Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_all_events_table1.tabular Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,10 +1,10 @@ ### MultiGPS output #Condition Name Index TotalSigCount SignalFraction -#Condition experiment 0 99.0 0.555 +#Condition cond 0 99.0 0.555 #Replicate ParentCond Name Index SigCount CtrlCount SigCtrlScaling SignalFraction -#Replicate experiment experiment:rep1 0 99.0 0 1 0.56 +#Replicate cond cond:1 0 99.0 0 1 0.56 # -#Point experiment_Sig experiment_Ctrl experiment_log2Fold experiment_log2P ActiveConds +#Point cond_Sig cond_Ctrl cond_log2Fold cond_log2P ActiveConds chr1:569927 14.3 0.0 3.838 -6.470 1 chr1:536042 1.0 0.0 0.014 -1.474 1 chr1:535151 1.0 0.0 0.014 -1.413 1 |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_all_events_table2.tabular --- a/test-data/hg19_all_events_table2.tabular Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_all_events_table2.tabular Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,10 +1,10 @@ ### MultiGPS output #Condition Name Index TotalSigCount SignalFraction -#Condition experiment 0 99.0 0.555 +#Condition cond 0 99.0 0.555 #Replicate ParentCond Name Index SigCount CtrlCount SigCtrlScaling SignalFraction -#Replicate experiment experiment:rep1 0 99.0 18.0 4.00 0.555 +#Replicate cond cond:1 0 99.0 18.0 4.00 0.555 # -#Point experiment_Sig experiment_Ctrl experiment_log2Fold experiment_log2P ActiveConds +#Point cond_Sig cond_Ctrl cond_log2Fold cond_log2P ActiveConds chr1:569927 14.3 0.0 3.838 -6.470 1 chr1:536042 1.0 0.0 0.014 -1.281 1 chr1:535151 1.0 0.0 0.014 -1.211 1 |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_output_bed1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_output_bed1.bed Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -0,0 +1,1 @@ +track name=multiGPS-cond description=multiGPS events cond |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_output_bed2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_output_bed2.bed Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -0,0 +1,1 @@ +track name=multiGPS-cond description=multiGPS events cond |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_output_html1.html --- a/test-data/hg19_output_html1.html Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_output_html1.html Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,13 +1,12 @@ <html> <body> -</p> <h2>Binding events</h2> <table> <tr> <th>Condition</th> <th>Events</th> <th>File</th> </tr> - <tr> <td>experiment</td> + <tr> <td>cond</td> <td>0</td> </tr> </table> @@ -19,7 +18,7 @@ <th>SignalFraction</th> <th>ReadDistributionModel</th> </tr> - <tr> <td>experiment rep1</td> + <tr> <td>cond 1</td> <td>99.0</td> <td>NA</td> <td>0.555</td> |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_output_html2.html --- a/test-data/hg19_output_html2.html Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_output_html2.html Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,13 +1,11 @@ <html> - <body> -</p> <h2>Binding events</h2> <table> <tr> <th>Condition</th> <th>Events</th> <th>File</th> </tr> - <tr> <td>experiment</td> + <tr> <td>cond</td> <td>0</td> </tr> </table> @@ -19,7 +17,7 @@ <th>SignalFraction</th> <th>ReadDistributionModel</th> </tr> - <tr> <td>experiment rep1</td> + <tr> <td>cond 1</td> <td>99.0</td> <td>4.000</td> <td>0.555</td> |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_replicates_counts1.tabular --- a/test-data/hg19_replicates_counts1.tabular Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_replicates_counts1.tabular Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,4 +1,4 @@ -Point experiment:rep1 +Point cond:1 chr1:569927 14 chr1:536042 1 chr1:535151 1 |
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| diff -r 7e0a12282c7f -r 028fafca04fa test-data/hg19_replicates_counts2.tabular --- a/test-data/hg19_replicates_counts2.tabular Tue Mar 28 12:24:56 2017 -0400 +++ b/test-data/hg19_replicates_counts2.tabular Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -1,4 +1,4 @@ -Point experiment:rep1 +Point cond:1 chr1:569927 14 chr1:536042 1 chr1:535151 1 |
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| diff -r 7e0a12282c7f -r 028fafca04fa tool-data/hg19.len --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hg19.len Sun Dec 22 12:11:33 2019 -0500 |
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| @@ -0,0 +1,15 @@ +chr1 249250621 +chr1_jh636052_fix 7283150 +chr1_jh636053_fix 1676126 +chr1_jh636054_fix 758378 +chr1_gl000192_random 547496 +chr1_gl383520_alt 366579 +chr1_gl383518_alt 182439 +chr1_gl949741_fix 151551 +chr1_gl383519_alt 110268 +chr1_gl000191_random 106433 +chr1_gl383517_fix 49352 +chr1_gl383516_fix 49316 +chr1_jh806575_fix 47409 +chr1_jh806573_fix 24680 +chr1_jh806574_fix 22982 |