diff fimo.xml @ 10:307b2f3559bf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd

--- 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">