# HG changeset patch
# User yating-l
# Date 1509991981 18000
# Node ID a65e52152476199a66e7310de8297ed3753221f3
# Parent  cb62314a6297fe9799e1323c1d3cace5e0cfc042
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f

diff -r cb62314a6297 -r a65e52152476 datatypes/binary/BigBed.py
--- a/datatypes/binary/BigBed.py	Fri Nov 03 17:08:19 2017 -0400
+++ b/datatypes/binary/BigBed.py	Mon Nov 06 13:13:01 2017 -0500
@@ -37,7 +37,7 @@
             self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink()
             self.extraSettings.update(self.database_settings)
         if "index_ix" in self.trackSettings and "index_ixx" in self.trackSettings:
-            self.trix_id = self.extraSettings.get("trix_id")
+            self.trix_id = self.trackSettings.get("trix_id")
             if not self.trix_id:
                 self.logger.info("Didn't specify the ID for Trix index for BigBed file: %s. \n Will use \"name\" as default", self.trackName)
                 self.trix_id = "name"
diff -r cb62314a6297 -r a65e52152476 datatypes/binary/BigBed.pyc
Binary file datatypes/binary/BigBed.pyc has changed
diff -r cb62314a6297 -r a65e52152476 datatypes/interval/BigPsl.pyc
Binary file datatypes/interval/BigPsl.pyc has changed
diff -r cb62314a6297 -r a65e52152476 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Fri Nov 03 17:08:19 2017 -0400
+++ b/hubArchiveCreator.xml	Mon Nov 06 13:13:01 2017 -0500
@@ -459,7 +459,8 @@
     </outputs>
 
     <tests>
-        <!-- Test with only the fasta file -->
+   
+       <!-- Test with only the fasta file -->
         <test>
             <param name="genome_name" value="Dbia3"/>
             <param name="fasta_file" value="common/dbia3.fa"/>
@@ -1374,9 +1375,9 @@
                 </extra_files>
                 <!-- check Trix index directory -->
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
-                             value="trix_index/blat_out.ix" />
+                             value="trix_index_files/blat_out.ix" />
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
-                             value="trix_index/blat_out.ixx" />
+                             value="trix_index_files/blat_out.ixx" />
             </output>
         </test>
 
@@ -1424,9 +1425,9 @@
                 </extra_files>
                 <!-- check Trix index directory -->
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
-                             value="trix_index/blast_out.ix" />
+                             value="trix_index_files/blast_out.ix" />
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
-                             value="trix_index/blast_out.ixx" />
+                             value="trix_index_files/blast_out.ixx" />
             </output>
         </test>
 
@@ -1444,7 +1445,7 @@
                         <param name="track_color" value="#000000"/>
                         <conditional name="add_trix_index">
                             <param name="add_trix_index_selector" value="yes" />
-                            <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
+                            <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
                             <param name="trix_id" value="name" />
                         </conditional>
                     </conditional>
@@ -1464,9 +1465,9 @@
 
                 <!-- check Trix index directory -->
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
-                             value="trix_index/blat_out.ix" />
+                             value="trix_index_files/blat_out.ix" />
                 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
-                             value="trix_index/blat_out.ixx" />
+                             value="trix_index_files/blat_out.ixx" />
             </output>
         </test>
         
diff -r cb62314a6297 -r a65e52152476 macros.xml
--- a/macros.xml	Fri Nov 03 17:08:19 2017 -0400
+++ b/macros.xml	Mon Nov 06 13:13:01 2017 -0500
@@ -63,14 +63,17 @@
                     type="data"
                     format="txt"
                     multiple="true"
+                    min="2"
+                    max="2"
                     label="Specify Trix index" 
                     help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator"
                 />
-            <yield />
+                <yield />
             </when>
             <when value="no">
             </when>
         </conditional>
     </xml>
 
+
 </macros>
\ No newline at end of file
diff -r cb62314a6297 -r a65e52152476 test-data/trix_index_files/bigbed_trackhub.html
--- a/test-data/trix_index_files/bigbed_trackhub.html	Fri Nov 03 17:08:19 2017 -0400
+++ b/test-data/trix_index_files/bigbed_trackhub.html	Mon Nov 06 13:13:01 2017 -0500
@@ -26,27 +26,14 @@
                 <ul>
                     
                 <li>
-                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
-                </li>
-                <li>
                     <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
                 </li>
                 <li>
-                    <a href="myHub/Dbia3/description.html">description.html</a>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
                 </li>
                 <li>
-                    trix
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
                 </li>
-                <ul>
-                    
-                <li>
-                    <a href="myHub/unknown/trix/pslToBigPsl_on_data_43.bb.bigbed.ix">pslToBigPsl_on_data_43.bb.bigbed.ix</a>
-                </li>
-                <li>
-                    <a href="myHub/unknown/trix/pslToBigPsl_on_data_43.bb.bigbed.ixx">pslToBigPsl_on_data_43.bb.bigbed.ixx</a>
-                </li>
-
-                </ul>
                 <li>
                     tracks
                 </li>
@@ -58,8 +45,21 @@
 
                 </ul>
                 <li>
-                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    trix
                 </li>
+                <ul>
+                    
+                <li>
+                    <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx">BLAT_alignment_bigbed.bigbed.ixx</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix">BLAT_alignment_bigbed.bigbed.ix</a>
+                </li>
+
+                </ul>
 
                 </ul>
 
diff -r cb62314a6297 -r a65e52152476 test-data/trix_index_files/blast_alignment_trackhub.html
--- a/test-data/trix_index_files/blast_alignment_trackhub.html	Fri Nov 03 17:08:19 2017 -0400
+++ b/test-data/trix_index_files/blast_alignment_trackhub.html	Mon Nov 06 13:13:01 2017 -0500
@@ -12,15 +12,27 @@
                 <ul>
                     
                 <li>
-                    unknown
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
                 </li>
                 <ul>
                     
                 <li>
-                    <a href="myHub/unknown/trackDb.txt">trackDb.txt</a>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
                 </li>
                 <li>
-                    <a href="myHub/unknown/groups.txt">groups.txt</a>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
                 </li>
                 <li>
                     tracks
@@ -33,34 +45,21 @@
 
                 </ul>
                 <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
                     trix
                 </li>
                 <ul>
                     
                 <li>
-                    <a href="myHub/unknown/trix/BLAST_alignment_bigpsl.bb.ix">BLAST_alignment_bigpsl.bb.ix</a>
+                    <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx">BLAST_alignment_bigpsl.bb.ixx</a>
                 </li>
                 <li>
-                    <a href="myHub/unknown/trix/BLAST_alignment_bigpsl.bb.ixx">BLAST_alignment_bigpsl.bb.ixx</a>
+                    <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix">BLAST_alignment_bigpsl.bb.ix</a>
                 </li>
 
                 </ul>
-                <li>
-                    tracks
-                </li>
-                <ul>
-                    
-                <li>
-                    <a href="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb">BLAST_alignment_bigpsl.bb</a>
-                </li>
-                
-                </ul>
-                <li>
-                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/description.html">description.html</a>
-                </li>
 
                 </ul>
 
diff -r cb62314a6297 -r a65e52152476 test-data/trix_index_files/blat_alignment_trackhub.html
--- a/test-data/trix_index_files/blat_alignment_trackhub.html	Fri Nov 03 17:08:19 2017 -0400
+++ b/test-data/trix_index_files/blat_alignment_trackhub.html	Mon Nov 06 13:13:01 2017 -0500
@@ -12,15 +12,27 @@
                 <ul>
                     
                 <li>
-                    unknown
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
                 </li>
                 <ul>
                     
                 <li>
-                    <a href="myHub/unknown/trackDb.txt">trackDb.txt</a>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
                 </li>
                 <li>
-                    <a href="myHub/unknown/groups.txt">groups.txt</a>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
                 </li>
                 <li>
                     tracks
@@ -33,34 +45,21 @@
 
                 </ul>
                 <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
                     trix
                 </li>
                 <ul>
                     
                 <li>
-                    <a href="myHub/unknown/trix/BLAT_alignment_bigpsl.bb.bigbed.ix">BLAT_alignment_bigpsl.bb.ix</a>
+                    <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix">BLAT_alignment_bigpsl.bb.ix</a>
                 </li>
                 <li>
-                    <a href="myHub/unknown/trix/BLAT_alignment_bigpsl.bb.bigbed.ixx">BLAT_alignment_bigpsl.bb.ixx</a>
+                    <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx">BLAT_alignment_bigpsl.bb.ixx</a>
                 </li>
 
                 </ul>
-                <li>
-                    tracks
-                </li>
-                <ul>
-                    
-                <li>
-                    <a href="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb">BLAT_alignment_bigpsl.bb</a>
-                </li>
-                
-                </ul>
-                <li>
-                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
-                </li>
-                <li>
-                    <a href="myHub/Dbia3/description.html">description.html</a>
-                </li>
 
                 </ul>
 
diff -r cb62314a6297 -r a65e52152476 tests.xml
--- a/tests.xml	Fri Nov 03 17:08:19 2017 -0400
+++ b/tests.xml	Mon Nov 06 13:13:01 2017 -0500
@@ -1,6 +1,59 @@
-<macro>
-    <xml name="test_cases">
-        <!-- Test with only the fasta file -->
+            #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
+                #set database = str($f.formatChoice.bedChoice.database)
+                #silent $extra_data_dict.update({"database": $database})
+                #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
+                    #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
+                        #if $i.element_identifier.endswith("ix")
+                            #$extra_data_dict.update({"index_ix": str($i)})
+                        #elif $i.element_identifier.endswith("ixx")
+                            #$extra_data_dict.update({"index_ixx": str($i)})
+                        #end if
+                    #end for
+                    ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
+                    ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
+                    ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
+                #end if
+                #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
+                                             $extra_data_dict)
+            #end if
+            #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
+                #set database = str($f.formatChoice.bedChoice.database)
+                #silent $extra_data_dict.update({"database": $database})
+                #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
+                    #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
+                        #if $i.element_identifier.endswith("ix")
+                            #$extra_data_dict.update({"index_ix": str($i)})
+                        #elif $i.element_identifier.endswith("ixx")
+                            #$extra_data_dict.update({"index_ixx": str($i)})
+                        #end if
+                    #end for
+                    ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
+                    ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
+                    ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
+                #end if
+                #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
+                                             $extra_data_dict)
+            #end if    
+            
+            #if $f.formatChoice.format_select == "bigbed"
+            #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
+                ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
+                ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
+                #for i in $f.formatChoice.add_trix_index.trix_index
+                    #if $i.element_identifier.endswith("ix")
+                        #$extra_data_dict.update({"index_ix": str($i)})
+                    #elif $i.element_identifier.endswith("ixx")
+                        #$extra_data_dict.update({"index_ixx": str($i)})
+                    #end if
+                #end for
+                #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
+                ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
+                ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
+            #end if
+            #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
+                                            $extra_data_dict)
+        #end if    
+       <!-- Test with only the fasta file -->
         <test>
             <param name="genome_name" value="Dbia3"/>
             <param name="fasta_file" value="common/dbia3.fa"/>
@@ -870,149 +923,3 @@
                 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
             </output>
         </test>
-
-        <!-- Test TrixIndex for Blat alignment track -->
-        <test>
-            <param name="genome_name" value="Dbia3"/>
-            <param name="fasta_file" value="common/dbia3.fa"/>
-            <repeat name="group">
-                <param name="group_name" value="Default group"/>
-                <repeat name="format">
-                    <conditional name="formatChoice">
-                        <param name="format_select" value="bed" />
-                        <conditional name="bedChoice">
-                            <param name="bed_select" value="bed_blat_alignment_option"/>
-                            <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
-                            <param name="longLabel" value="BLAT alignment" />
-                            <param name="track_color" value="#000000"/>
-                            <param name="database" value="NCBI" />
-                            <conditional name="add_trix_index">
-                                <param name="add_trix_index_selector" value="yes" />
-                                <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
-                            </conditional>
-                        </conditional>
-                    </conditional>
-                </repeat>
-            </repeat>
-            <param name="debug_mode" value="true" />
-            <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
-                <extra_files type="file"
-                             name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
-                             value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
-                             compare="sim_size"
-                />
-                <expand macro="verify_hub_structure" test="bed_blat_alignment" />
-                <!-- check additional trackDb settings for BLAT -->
-                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
-                    <assert_contents>
-                        <has_text text="searchIndex"/>
-                        <has_text text="searchTrix"/>
-                        <has_text text="url"/>
-                        <has_text text="urlLabel"/>
-                        <has_text text="iframeUrl"/>
-                        <has_text text="iframeOptions"/>
-                    </assert_contents>
-                </extra_files>
-                <!-- check Trix index directory -->
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
-                             value="trix_index/blat_out.ix" />
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
-                             value="trix_index/blat_out.ixx" />
-            </output>
-        </test>
-
-        <!-- Test TrixIndex for BLAST Alignment -->
-        <test>
-            <param name="genome_name" value="Dbia3"/>
-            <param name="fasta_file" value="common/dbia3.fa"/>
-            <repeat name="group">
-                <param name="group_name" value="Default group"/>
-                <repeat name="format">
-                    <conditional name="formatChoice">
-                        <param name="format_select" value="bed" />
-                        <conditional name="bedChoice">
-                            <param name="bed_select" value="bed_blast_alignment_option"/>
-                            <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
-                            <param name="longLabel" value="BLAST alignment" />
-                            <param name="track_color" value="#000000"/>
-                            <param name="database" value="NCBI" />
-                            <conditional name="add_trix_index">
-                                <param name="add_trix_index_selector" value="yes" />
-                                <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
-                            </conditional>
-                        </conditional>
-                    </conditional>
-                </repeat>
-            </repeat>
-            <param name="debug_mode" value="true" />
-            <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
-                <extra_files type="file"
-                             name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
-                             value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
-                             compare="sim_size"
-                />
-                <expand macro="verify_hub_structure" test="bed_blast_alignment" />
-                <!-- check additional trackDb settings for BLAST -->
-                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
-                    <assert_contents>
-                        <has_text text="searchIndex"/>
-                        <has_text text="searchTrix"/>
-                        <has_text text="url"/>
-                        <has_text text="urlLabel"/>
-                        <has_text text="iframeUrl"/>
-                        <has_text text="iframeOptions"/>
-                    </assert_contents>
-                </extra_files>
-                <!-- check Trix index directory -->
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
-                             value="trix_index/blast_out.ix" />
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
-                             value="trix_index/blast_out.ixx" />
-            </output>
-        </test>
-
-        <!-- Test TrixIndex for BigBed -->
-        <test>
-            <param name="genome_name" value="Dbia3"/>
-            <param name="fasta_file" value="common/dbia3.fa"/>
-            <repeat name="group">
-                <param name="group_name" value="Default group"/>
-                <repeat name="format">
-                    <conditional name="formatChoice">
-                        <param name="format_select" value="bigbed"/>
-                        <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
-                        <param name="longLabel" value="bigBed" />
-                        <param name="track_color" value="#000000"/>
-                        <conditional name="add_trix_index">
-                            <param name="add_trix_index_selector" value="yes" />
-                            <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
-                            <param name="trix_id" value="name" />
-                        </conditional>
-                    </conditional>
-                </repeat>
-            </repeat>
-            <param name="debug_mode" value="true" />
-            <output name="output" file="trix_index_files/bigbed_trackhub.html">
-                <extra_files type="file"
-                             name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
-                             value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
-                             compare="sim_size"
-                />
-                <expand macro="verify_hub_structure" test="big_bed">
-                    <has_text text="searchIndex"/>
-                    <has_text text="searchTrix"/>
-                </expand>
-
-                <!-- check Trix index directory -->
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
-                             value="trix_index/blat_out.ix" />
-                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
-                             value="trix_index/blat_out.ixx" />
-            </output>
-        </test>
-
-        <!-- Test for big files? -->
-
-        <!-- Find tests that should fail -->
-    </xml>
-</macro>
diff -r cb62314a6297 -r a65e52152476 util/index/TrixIndex.py
--- a/util/index/TrixIndex.py	Fri Nov 03 17:08:19 2017 -0400
+++ b/util/index/TrixIndex.py	Mon Nov 06 13:13:01 2017 -0500
@@ -14,7 +14,7 @@
         self.trackName = trackName
         self.mySpecieFolderPath = mySpecieFolderPath
         self.index_settings = collections.OrderedDict()
-        self.trixId = trixId
+        self.trixId = trixId.rstrip()
         
 
     def setExtLink(self):
diff -r cb62314a6297 -r a65e52152476 util/index/TrixIndex.pyc
Binary file util/index/TrixIndex.pyc has changed