# HG changeset patch # User iuc # Date 1524229424 14400 # Node ID 6095db40281111423f368b9584e34ca7dd828464 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 diff -r 000000000000 -r 6095db402811 get_meme_motif_databases.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_meme_motif_databases.py Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,11 @@ +import os + + +def get_meme_motif_database_options(file_path): + options = [] + if not os.path.isdir(file_path): + return options + for i, file_name in enumerate(os.listdir(file_path)): + full_path = os.path.join(file_path, file_name) + options.append((file_name, full_path, i == 0)) + return options diff -r 000000000000 -r 6095db402811 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,11 @@ + + + 4.11.2 + + + graphicsmagick + meme + + + + diff -r 000000000000 -r 6095db402811 meme_chip.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meme_chip.xml Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,224 @@ + + - motif discovery, enrichment analysis and clustering on large nucleotide datasets + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value == True + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. +Before using, be sure to review, agree, and comply with the license.** + +MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. + +If you want to specify sequence weights, you must include them at the top of your input FASTA file. + +MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences). +MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly +in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the +probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns +with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and +outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number +of occurrences, and description for each motif. + +.. class:: infomark + +For detailed information on MEME, click here_, or view the license_. + +.. _here: http://meme-suite.org/doc/meme.html?man_type=web +.. _license: http://meme-suite.org/doc/copyright.html?man_type=web + + + + 10.1093/bioinformatics/btr189 + + + diff -r 000000000000 -r 6095db402811 meme_motif_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meme_motif_databases.loc.sample Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,7 @@ +# This file has the format (white space characters are TAB characters): +# +# +# +#So, meme_motif_databases.loc could look something like this: +# +#2017_12 2017_12 /meme_motif_databases/2017_12 December 2017 diff -r 000000000000 -r 6095db402811 test-data/input1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.fasta Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTCAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG diff -r 000000000000 -r 6095db402811 test-data/output1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.html Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,86 @@ + + + + + MEME ChIP + + + +

+ If you use MEME-ChIP in your research, please cite the following paper:
+

+ +
+ Motifs +   |   + Programs +   |   + Input Files +   |   + Program information +
+ + +

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+ + + + + +

Motifs

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+

The significant motifs + (E-value ≤ ) + found by the programs MEME, DREME and CentriMo; + clustered by similarity and ordered by E-value.

+ +
+ Expand All Clusters + Collapse All Clusters +
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+ +
+ +

Programs

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+ + +

Input Files

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+ +
+ +

Motifs

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+ +
+ +
+
+
MEME-ChIP version
+ + (Release date: )
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+ +
+
Reference
+
+
Command line summary
+ + +
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+ + diff -r 000000000000 -r 6095db402811 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Apr 20 09:03:44 2018 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+