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changeset 9:794b2859c286 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 20:39:45 -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(-) [+]
line wrap: on
line diff
--- /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>