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changeset 10:307b2f3559bf draft

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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>