# HG changeset patch
# User bgruening
# Date 1580168225 18000
# Node ID 7bbb7bf6304f24aa6b1639fce3314e23597552c5
# Parent  20429f4c1b95e784606181161a0419d3167efbd0
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit afbe0da7a518d6fc60ea066917b1e567c8c42391"

diff -r 20429f4c1b95 -r 7bbb7bf6304f graphprot_predict_wrapper.py
--- a/graphprot_predict_wrapper.py	Wed Jan 22 10:14:41 2020 -0500
+++ b/graphprot_predict_wrapper.py	Mon Jan 27 18:37:05 2020 -0500
@@ -186,11 +186,11 @@
     # Read in FASTA sequences to check for uppercase sequences.
     seqs_dic = gplib.read_fasta_into_dic(args.in_fa)
     c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic)
-    assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept))"
+    assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept)"
     if not args.ws_pred:
         # Check for lowercase sequences.
         c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic)
-        assert not c_lc_nt, "lowercase nucleotides not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept))"
+        assert not c_lc_nt, "lowercase nucleotides in input .fa not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept)"
     # Check .bed.
     if args.genomic_sites_bed:
         # An array of checks, marvelous.
diff -r 20429f4c1b95 -r 7bbb7bf6304f graphprot_train_predict.xml
--- a/graphprot_train_predict.xml	Wed Jan 22 10:14:41 2020 -0500
+++ b/graphprot_train_predict.xml	Mon Jan 27 18:37:05 2020 -0500
@@ -154,7 +154,7 @@
         </data>
 
         <data name="str_motif_out_file" format="txt" from_work_dir="GraphProt.structure_motif" label="${tool.name} on ${on_string}: GraphProt structure motif text file">
-            <filter>action_type["action_type_selector"] == "train" and not action_type["training_options"]["disable_motifs"]</filter>
+            <filter>action_type["action_type_selector"] == "train" and not action_type["training_options"]["disable_motifs"] and action_type["train_str_model"]</filter>
         </data>
 
         <data name="str_motif_png_out_file" format="png" from_work_dir="GraphProt.structure_motif.png" label="${tool.name} on ${on_string}: GraphProt structure motif png file">
@@ -193,7 +193,7 @@
 
     <tests>
 
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="4">
             <param name="action_type_selector" value="train"/>
             <param name="pos_fasta_file" value="test_positives.train.fa" ftype="fasta"/>
             <param name="neg_fasta_file" value="test_negatives.train.fa" ftype="fasta"/>