| Previous changeset 8:e8b209806a20 (2016-11-14) Next changeset 10:b8c05adb68da (2017-08-23) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd |
|
modified:
meme.xml test-data/fimo_output_html_1.html test-data/fimo_output_html_2.html test-data/fimo_output_xml_1.xml test-data/fimo_output_xml_2.xml test-data/meme_output_html_1.html test-data/meme_output_html_2.html test-data/meme_output_txt_1.txt test-data/meme_output_txt_2.txt test-data/meme_output_xml_1.xml test-data/meme_output_xml_2.xml tool_data_table_conf.xml.sample |
|
added:
macros.xml |
|
removed:
tool_dependencies.xml |
| b |
| diff -r e8b209806a20 -r 794b2859c286 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.3.23">graphicsmagick</requirement> + <requirement type="package" version="4.11.2">meme</requirement> + </requirements> + </xml> +</macros> + |
| b |
| diff -r e8b209806a20 -r 794b2859c286 meme.xml --- a/meme.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/meme.xml Thu Jun 29 20:39:45 2017 -0400 |
| [ |
| b'@@ -1,87 +1,78 @@\n-<tool id="meme_meme" name="MEME" version="4.11.1.0">\n+<tool id="meme_meme" name="MEME" version="4.11.2.0">\n <description>- Multiple Em for Motif Elicitation</description>\n- <requirements>\n- <requirement type="package" version="1.3.20">graphicsmagick</requirement>\n- <requirement type="package" version="4.11.1">meme</requirement>\n- </requirements>\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <!-- In case the return code has not been set propery check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n- <command>\n- <![CDATA[\n- meme "$input1"\n- -o "${html_outfile.files_path}"\n- -nostatus\n- -maxsize 1000000\n- #if str( $options_type.options_type_selector ) == \'advanced\':\n- -sf "${ str( $options_type.sf ).replace( \' \', \'_\' ) }"\n- -${options_type.alphabet_type.alphabet_type_selector}\n- -mod "${options_type.mod_type.mod_type_selector}"\n- -nmotifs "${options_type.nmotifs}"\n- -wnsites "${options_type.wnsites}"\n- #if $options_type.evt < float(\'inf\'):\n- -evt "${options_type.evt}"\n- #end if\n- #if str( $options_type.mod_type.mod_type_selector ) != \'oops\':\n- #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == \'nsites\':\n- -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"\n- #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == \'min_max_sites\':\n- -minsites "${options_type.mod_type.motif_occurrence_type.minsites}"\n- -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"\n- #end if\n- #end if\n- #if str( $options_type.motif_width_type.motif_width_type_selector ) == \'exact\':\n- -w "${options_type.motif_width_type.width}"\n- #else\n- -minw "${options_type.motif_width_type.minw}"\n- -maxw "${options_type.motif_width_type.maxw}"\n- #end if\n- #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == \'nomatrim\':\n- -nomatrim\n- #else\n- -wg "${options_type.motif_trim_type.wg}"\n- -ws "${options_type.motif_trim_type.ws}"\n- ${options_type.motif_trim_type.noendgaps}\n- #end if\n- #if str( $options_type.bfile ) != \'None\':\n- -bfile "${options_type.bfile}"\n- #end if\n- #if str( $options_type.pspfile ) != \'None\':\n- -psp "${options_type.pspfile}"\n- #end if\n- #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":\n- ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}\n- #end if\n- -maxiter "${options_type.maxiter}"\n- -distance "${options_type.distance}"\n- -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"\n- #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != \'addone\':\n- -b "${options_type.alphabet_type.prior_type.prior_b}"\n- #if str( $options_type.alphabet_type.prior_type.plib ) != \'None\':\n- -plib "${options_type.alphabet_type.prior_type.plib}"\n- #end if\n- #end if\n- #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == \'cons\':\n- -cons "${options_type.alphabet_type.spmap_type.cons}"\n- #else\n- -spma'..b'ector ) == \'x_branch\':\n- -x_branch\n- -bfactor "${options_type.branching_type.bfactor}"\n- -heapsize "${options_type.branching_type.heapsize}"\n- #end if\n- #end if\n- && mv ${html_outfile.files_path}/meme.html ${html_outfile}\n- && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}\n- && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}\n- ]]>\n- </command>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+meme \'$input1\'\n+-o \'${html_outfile.files_path}\'\n+-nostatus\n+-maxsize 1000000\n+#if str( $options_type.options_type_selector ) == \'advanced\':\n+ -sf \'${ str( $options_type.sf ).replace( " ", "_" ) }\'\n+ -${options_type.alphabet_type.alphabet_type_selector}\n+ -mod \'${options_type.mod_type.mod_type_selector}\'\n+ -nmotifs \'${options_type.nmotifs}\'\n+ -wnsites \'${options_type.wnsites}\'\n+ #if $options_type.evt < float(\'inf\'):\n+ -evt \'${options_type.evt}\'\n+ #end if\n+ #if str( $options_type.mod_type.mod_type_selector ) != \'oops\':\n+ #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == \'nsites\':\n+ -nsites \'${options_type.mod_type.motif_occurrence_type.nsites}\'\n+ #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == \'min_max_sites\':\n+ -minsites \'${options_type.mod_type.motif_occurrence_type.minsites}\'\n+ -maxsites \'${options_type.mod_type.motif_occurrence_type.maxsites}\'\n+ #end if\n+ #end if\n+ #if str( $options_type.motif_width_type.motif_width_type_selector ) == \'exact\':\n+ -w \'${options_type.motif_width_type.width}\'\n+ #else\n+ -minw \'${options_type.motif_width_type.minw}\'\n+ -maxw \'${options_type.motif_width_type.maxw}\'\n+ #end if\n+ #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == \'nomatrim\':\n+ -nomatrim\n+ #else\n+ -wg \'${options_type.motif_trim_type.wg}\'\n+ -ws \'${options_type.motif_trim_type.ws}\'\n+ ${options_type.motif_trim_type.noendgaps}\n+ #end if\n+ #if str( $options_type.bfile ) != \'None\':\n+ -bfile \'${options_type.bfile}\'\n+ #end if\n+ #if str( $options_type.pspfile ) != \'None\':\n+ -psp \'${options_type.pspfile}\'\n+ #end if\n+ #if str( $options_type.alphabet_type.alphabet_type_selector ) == \'dna\':\n+ ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}\n+ #end if\n+ -maxiter \'${options_type.maxiter}\'\n+ -distance \'${options_type.distance}\'\n+ -prior \'${options_type.alphabet_type.prior_type.prior_type_selector}\'\n+ #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != \'addone\':\n+ -b \'${options_type.alphabet_type.prior_type.prior_b}\'\n+ #if str( $options_type.alphabet_type.prior_type.plib ) != \'None\':\n+ -plib \'${options_type.alphabet_type.prior_type.plib}\'\n+ #end if\n+ #end if\n+ #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == \'cons\':\n+ -cons \'${options_type.alphabet_type.spmap_type.cons}\'\n+ #else\n+ -spmap \'${options_type.alphabet_type.spmap_type.spmap_type_selector}\'\n+ -spfuzz \'${options_type.alphabet_type.spmap_type.spfuzz}\'\n+ #end if\n+ #if str( $options_type.branching_type.branching_type_selector ) == \'x_branch\':\n+ -x_branch\n+ -bfactor \'${options_type.branching_type.bfactor}\'\n+ -heapsize \'${options_type.branching_type.heapsize}\'\n+ #end if\n+#end if\n+&& mv \'${html_outfile.files_path}/meme.html\' \'${html_outfile}\'\n+&& mv \'${html_outfile.files_path}/meme.txt\' \'${txt_outfile}\'\n+&& mv \'${html_outfile.files_path}/meme.xml\' \'${xml_outfile}\'\n+ ]]></command>\n <inputs>\n <param format="fasta" name="input1" type="data" label="Sequences"/>\n <conditional name="options_type">\n' |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/fimo_output_html_1.html --- a/test-data/fimo_output_html_1.html Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/fimo_output_html_1.html Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -25,9 +25,6 @@ <center><big><b>FIMO - Motif search tool</b></big></center> <hr> <p> -FIMO version 4.11.1, (Release date: Fri Jan 15 12:51:59 2016 -0800) -</p> -<p> For further information on how to interpret these results or to get a copy of the FIMO software please access <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/fimo_output_html_2.html --- a/test-data/fimo_output_html_2.html Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/fimo_output_html_2.html Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -25,9 +25,6 @@ <center><big><b>FIMO - Motif search tool</b></big></center> <hr> <p> -FIMO version 4.11.1, (Release date: Fri Jan 15 12:51:59 2016 -0800) -</p> -<p> For further information on how to interpret these results or to get a copy of the FIMO software please access <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/fimo_output_xml_1.xml --- a/test-data/fimo_output_xml_1.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/fimo_output_xml_1.xml Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -1,9 +1,5 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!-- Begin document body --> -<fimo version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800"> - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" -> <settings> <setting name="allow clobber">false</setting> <setting name="compute q-values">true</setting> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/fimo_output_xml_2.xml --- a/test-data/fimo_output_xml_2.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/fimo_output_xml_2.xml Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -1,9 +1,5 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!-- Begin document body --> -<fimo version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800"> - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" -> <settings> <setting name="allow clobber">false</setting> <setting name="compute q-values">false</setting> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_html_1.html --- a/test-data/meme_output_html_1.html Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_html_1.html Thu Jun 29 20:39:45 2017 -0400 |
| [ |
| @@ -7,8 +7,6 @@ // @JSON_VAR data var data = { "program": "MEME", - "version": "4.11.1", - "release": "Fri Jan 15 12:51:59 2016 -0800", "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ "meme", |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_html_2.html --- a/test-data/meme_output_html_2.html Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_html_2.html Thu Jun 29 20:39:45 2017 -0400 |
| [ |
| @@ -7,8 +7,6 @@ // @JSON_VAR data var data = { "program": "MEME", - "version": "4.11.1", - "release": "Fri Jan 15 12:51:59 2016 -0800", "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ "meme", |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_txt_1.txt --- a/test-data/meme_output_txt_1.txt Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_txt_1.txt Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ ******************************************************************************** MEME - Motif discovery tool ******************************************************************************** -MEME version 4.11.1 (Release date: Fri Jan 15 12:51:59 2016 -0800) +MEME version 4.11.2 (Release date: Thu May 05 14:58:55 2016 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . @@ -28,7 +28,7 @@ ******************************************************************************** TRAINING SET ******************************************************************************** -DATAFILE= +DATAFILE= /tmp/tmpCNK6l0/files/000/dataset_22.dat ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme +command: meme /tmp/tmpCNK6l0/files/000/dataset_22.dat -o /tmp/tmpCNK6l0/job_working_directory/000/11/dataset_23_files -nostatus -maxsize 1000000 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -267,7 +267,7 @@ -Time +Time 0.72 secs. ******************************************************************************** @@ -320,6 +320,6 @@ Stopped because requested number of motifs (1) found. ******************************************************************************** -CPU: +CPU: bigsky ******************************************************************************** |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_txt_2.txt --- a/test-data/meme_output_txt_2.txt Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_txt_2.txt Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ ******************************************************************************** MEME - Motif discovery tool ******************************************************************************** -MEME version 4.11.1 (Release date: Fri Jan 15 12:51:59 2016 -0800) +MEME version 4.11.2 (Release date: Thu May 05 14:58:55 2016 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme +command: meme /tmp/tmpCNK6l0/files/000/dataset_26.dat -o /tmp/tmpCNK6l0/job_working_directory/000/14/dataset_28_files -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -evt inf -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /tmp/tmpCNK6l0/files/000/dataset_27.dat -spmap uni -spfuzz 0.5 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -69,7 +69,7 @@ data: n= 1500 N= 30 shuffle= -1 strands: + sample: seed= 0 ctfrac= -1 maxwords= -1 -Dirichlet mixture priors file: +Dirichlet mixture priors file: dataset_27.dat Letter frequencies in dataset: A 0.294 C 0.231 G 0.257 T 0.217 Background letter frequencies (from dataset with add-one prior applied): @@ -261,7 +261,7 @@ -Time +Time 0.32 secs. ******************************************************************************** @@ -314,6 +314,6 @@ Stopped because requested number of motifs (1) found. ******************************************************************************** -CPU: +CPU: bigsky ******************************************************************************** |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_xml_1.xml --- a/test-data/meme_output_xml_1.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_xml_1.xml Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -161,7 +161,7 @@ ]> <!-- Begin document body --> -<MEME version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800"> +<MEME version="4.11.2" release="Thu May 05 14:58:55 2016 -0700"> <training_set datafile="/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat" length="30"> <alphabet name="Protein" like="protein"> <letter id="A" symbol="A" name="Alanine" colour="0000CC"/> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 test-data/meme_output_xml_2.xml --- a/test-data/meme_output_xml_2.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/test-data/meme_output_xml_2.xml Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -161,7 +161,7 @@ ]> <!-- Begin document body --> -<MEME version="4.11.1" release="Fri Jan 15 12:51:59 2016 -0800"> +<MEME version="4.11.2" release="Thu May 05 14:58:55 2016 -0700"> <training_set datafile="Galaxy_FASTA_Input" length="30"> <alphabet name="DNA" like="dna"> <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon Nov 14 13:17:41 2016 -0500 +++ b/tool_data_table_conf.xml.sample Thu Jun 29 20:39:45 2017 -0400 |
| b |
| @@ -1,6 +1,6 @@ <tables> <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> |
| b |
| diff -r e8b209806a20 -r 794b2859c286 tool_dependencies.xml --- a/tool_dependencies.xml Mon Nov 14 13:17:41 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="f2855f4cbc8f" name="package_graphicsmagick_1_3_20" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="meme" version="4.11.1"> - <repository changeset_revision="f585fa3ee66b" name="package_meme_4_11_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |