Mercurial > repos > iuc > meme_meme
changeset 9:794b2859c286 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2017 20:39:45 -0400 |
| parents | e8b209806a20 |
| children | b8c05adb68da |
| files | macros.xml 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 tool_dependencies.xml |
| diffstat | 14 files changed, 97 insertions(+), 123 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 29 20:39:45 2017 -0400 @@ -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> +
--- a/meme.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/meme.xml Thu Jun 29 20:39:45 2017 -0400 @@ -1,87 +1,78 @@ -<tool id="meme_meme" name="MEME" version="4.11.1.0"> +<tool id="meme_meme" name="MEME" version="4.11.2.0"> <description>- Multiple Em for Motif Elicitation</description> - <requirements> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> - <requirement type="package" version="4.11.1">meme</requirement> - </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> - <![CDATA[ - meme "$input1" - -o "${html_outfile.files_path}" - -nostatus - -maxsize 1000000 - #if str( $options_type.options_type_selector ) == 'advanced': - -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }" - -${options_type.alphabet_type.alphabet_type_selector} - -mod "${options_type.mod_type.mod_type_selector}" - -nmotifs "${options_type.nmotifs}" - -wnsites "${options_type.wnsites}" - #if $options_type.evt < float('inf'): - -evt "${options_type.evt}" - #end if - #if str( $options_type.mod_type.mod_type_selector ) != 'oops': - #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': - -nsites "${options_type.mod_type.motif_occurrence_type.nsites}" - #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': - -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" - -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}" - #end if - #end if - #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': - -w "${options_type.motif_width_type.width}" - #else - -minw "${options_type.motif_width_type.minw}" - -maxw "${options_type.motif_width_type.maxw}" - #end if - #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': - -nomatrim - #else - -wg "${options_type.motif_trim_type.wg}" - -ws "${options_type.motif_trim_type.ws}" - ${options_type.motif_trim_type.noendgaps} - #end if - #if str( $options_type.bfile ) != 'None': - -bfile "${options_type.bfile}" - #end if - #if str( $options_type.pspfile ) != 'None': - -psp "${options_type.pspfile}" - #end if - #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna": - ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} - #end if - -maxiter "${options_type.maxiter}" - -distance "${options_type.distance}" - -prior "${options_type.alphabet_type.prior_type.prior_type_selector}" - #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': - -b "${options_type.alphabet_type.prior_type.prior_b}" - #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': - -plib "${options_type.alphabet_type.prior_type.plib}" - #end if - #end if - #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': - -cons "${options_type.alphabet_type.spmap_type.cons}" - #else - -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}" - -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}" - #end if - #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': - -x_branch - -bfactor "${options_type.branching_type.bfactor}" - -heapsize "${options_type.branching_type.heapsize}" - #end if - #end if - && mv ${html_outfile.files_path}/meme.html ${html_outfile} - && mv ${html_outfile.files_path}/meme.txt ${txt_outfile} - && mv ${html_outfile.files_path}/meme.xml ${xml_outfile} - ]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +meme '$input1' +-o '${html_outfile.files_path}' +-nostatus +-maxsize 1000000 +#if str( $options_type.options_type_selector ) == 'advanced': + -sf '${ str( $options_type.sf ).replace( " ", "_" ) }' + -${options_type.alphabet_type.alphabet_type_selector} + -mod '${options_type.mod_type.mod_type_selector}' + -nmotifs '${options_type.nmotifs}' + -wnsites '${options_type.wnsites}' + #if $options_type.evt < float('inf'): + -evt '${options_type.evt}' + #end if + #if str( $options_type.mod_type.mod_type_selector ) != 'oops': + #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': + -nsites '${options_type.mod_type.motif_occurrence_type.nsites}' + #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': + -minsites '${options_type.mod_type.motif_occurrence_type.minsites}' + -maxsites '${options_type.mod_type.motif_occurrence_type.maxsites}' + #end if + #end if + #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': + -w '${options_type.motif_width_type.width}' + #else + -minw '${options_type.motif_width_type.minw}' + -maxw '${options_type.motif_width_type.maxw}' + #end if + #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': + -nomatrim + #else + -wg '${options_type.motif_trim_type.wg}' + -ws '${options_type.motif_trim_type.ws}' + ${options_type.motif_trim_type.noendgaps} + #end if + #if str( $options_type.bfile ) != 'None': + -bfile '${options_type.bfile}' + #end if + #if str( $options_type.pspfile ) != 'None': + -psp '${options_type.pspfile}' + #end if + #if str( $options_type.alphabet_type.alphabet_type_selector ) == 'dna': + ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} + #end if + -maxiter '${options_type.maxiter}' + -distance '${options_type.distance}' + -prior '${options_type.alphabet_type.prior_type.prior_type_selector}' + #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': + -b '${options_type.alphabet_type.prior_type.prior_b}' + #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': + -plib '${options_type.alphabet_type.prior_type.plib}' + #end if + #end if + #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': + -cons '${options_type.alphabet_type.spmap_type.cons}' + #else + -spmap '${options_type.alphabet_type.spmap_type.spmap_type_selector}' + -spfuzz '${options_type.alphabet_type.spmap_type.spfuzz}' + #end if + #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': + -x_branch + -bfactor '${options_type.branching_type.bfactor}' + -heapsize '${options_type.branching_type.heapsize}' + #end if +#end if +&& mv '${html_outfile.files_path}/meme.html' '${html_outfile}' +&& mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}' +&& mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}' + ]]></command> <inputs> <param format="fasta" name="input1" type="data" label="Sequences"/> <conditional name="options_type">
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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>
--- 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",
--- 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",
--- 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 @@ -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 ********************************************************************************
--- 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 @@ -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 ********************************************************************************
--- 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 @@ -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"/>
--- 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 @@ -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"/>
--- 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 @@ -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>
--- a/tool_dependencies.xml Mon Nov 14 13:17:41 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>