Mercurial > repos > iuc > meme_fimo
changeset 10:307b2f3559bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2017 20:39:58 -0400 |
| parents | 40b8472e91ca |
| children | c470b36b592d |
| files | fimo.xml macros.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, 76 insertions(+), 102 deletions(-) [+] |
line wrap: on
line diff
--- a/fimo.xml Mon Nov 14 13:17:22 2016 -0500 +++ b/fimo.xml Thu Jun 29 20:39:58 2017 -0400 @@ -1,66 +1,57 @@ -<tool id="meme_fimo" name="FIMO" version="4.11.1.0"> +<tool id="meme_fimo" name="FIMO" version="4.11.2.0"> <description>- Scan a set of sequences for motifs.</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[ - mkdir -p output && - python $__tool_directory__/fimo_wrapper.py - --input_motifs "${input_motifs}" - #if str($fasta_type.fasta_type_selector) == 'history': - --input_fasta "${fasta_type.input_database}" - #else: - --input_fasta "${fasta_type.input_database.fields.path}" - #end if - --options_type $options_type.options_type_selector - #if str($options_type.options_type_selector) == 'advanced': - --alpha "${options_type.alpha}" - #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': - --bgfile "motif-file" - #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': - --bgfile "${options_type.bgfile_type.bgfile}" - #end if - ${options_type.max_strand} - --max_stored_scores "${options_type.max_stored_scores}" - #if str($options_type.motifs_cond.motifs_selector) == 'no': - #for $motif in $options_type.motifs: - --motif "${motif.motif}" - #end for - #end if - --output_separate_motifs ${options_type.output_separate_motifs} - --motif_pseudo "${options_type.motif_pseudo}" - ${options_type.no_qvalue} - ${options_type.norc} - #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': - --parse_genomic_coord 'yes' - --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} - #end if - #if str($options_type.psp_cond.psp_selector) == 'yes': - --input_psp "${input_psp}" - #end if - #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': - --input_prior_dist "${input_prior_dist}" - #end if - ${options_type.qv_thresh} - --thresh ${options_type.thresh} - #end if - --output_path '${html_outfile.files_path}' - --html_output "${html_outfile}" - --interval_output '${interval_outfile}' - --txt_output "${txt_outfile}" - --xml_output "${xml_outfile}" - --gff_output "${gff_outfile}" - ]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +mkdir -p output && +python '$__tool_directory__/fimo_wrapper.py' +--input_motifs '${input_motifs}' +#if str($fasta_type.fasta_type_selector) == 'history': + --input_fasta '${fasta_type.input_database}' +#else: + --input_fasta '${fasta_type.input_database.fields.path}' +#end if +--options_type $options_type.options_type_selector +#if str($options_type.options_type_selector) == 'advanced': + --alpha '${options_type.alpha}' + #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': + --bgfile 'motif-file' + #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': + --bgfile '${options_type.bgfile_type.bgfile}' + #end if + ${options_type.max_strand} + --max_stored_scores '${options_type.max_stored_scores}' + #if str($options_type.motifs_cond.motifs_selector) == 'no': + #for $motif in $options_type.motifs: + --motif '${motif.motif}' + #end for + #end if + --output_separate_motifs ${options_type.output_separate_motifs} + --motif_pseudo '${options_type.motif_pseudo}' + ${options_type.no_qvalue} + ${options_type.norc} + #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': + --parse_genomic_coord 'yes' + --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} + #end if + #if str($options_type.psp_cond.psp_selector) == 'yes': + --input_psp '${input_psp}' + #end if + #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': + --input_prior_dist '${input_prior_dist}' + #end if + ${options_type.qv_thresh} + --thresh ${options_type.thresh} +#end if +--output_path '${html_outfile.files_path}' +--html_output '${html_outfile}' +--interval_output '${interval_outfile}' +--txt_output '${txt_outfile}' +--xml_output '${xml_outfile}' +--gff_output '${gff_outfile}' + ]]></command> <inputs> <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/> <conditional name="fasta_type">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 29 20:39:58 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/test-data/fimo_output_html_1.html Mon Nov 14 13:17:22 2016 -0500 +++ b/test-data/fimo_output_html_1.html Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/fimo_output_html_2.html Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/fimo_output_xml_1.xml Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/fimo_output_xml_2.xml Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_html_1.html Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_html_2.html Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_txt_1.txt Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_txt_2.txt Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_xml_1.xml Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/test-data/meme_output_xml_2.xml Thu Jun 29 20:39:58 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 13:17:22 2016 -0500 +++ b/tool_data_table_conf.xml.sample Thu Jun 29 20:39:58 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 13:17:22 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>