Mercurial > repos > yating-l > hubarchivecreator

comparison tests.xml @ 85:a65e52152476 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
parents cb62314a6297
children
comparison
equal deleted inserted replaced
84:cb62314a6297 85:a65e52152476
1 <macro> 1 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
2 <xml name="test_cases"> 2 #set database = str($f.formatChoice.bedChoice.database)
3 <!-- Test with only the fasta file --> 3 #silent $extra_data_dict.update({"database": $database})
4 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
5 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
6 #if $i.element_identifier.endswith("ix")
7 #$extra_data_dict.update({"index_ix": str($i)})
8 #elif $i.element_identifier.endswith("ixx")
9 #$extra_data_dict.update({"index_ixx": str($i)})
10 #end if
11 #end for
12 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
13 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
14 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
15 #end if
16 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
17 $extra_data_dict)
18 #end if
19 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
20 #set database = str($f.formatChoice.bedChoice.database)
21 #silent $extra_data_dict.update({"database": $database})
22 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
23 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
24 #if $i.element_identifier.endswith("ix")
25 #$extra_data_dict.update({"index_ix": str($i)})
26 #elif $i.element_identifier.endswith("ixx")
27 #$extra_data_dict.update({"index_ixx": str($i)})
28 #end if
29 #end for
30 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
31 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
32 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
33 #end if
34 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
35 $extra_data_dict)
36 #end if
37
38 #if $f.formatChoice.format_select == "bigbed"
39 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
40 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
41 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
42 #for i in $f.formatChoice.add_trix_index.trix_index
43 #if $i.element_identifier.endswith("ix")
44 #$extra_data_dict.update({"index_ix": str($i)})
45 #elif $i.element_identifier.endswith("ixx")
46 #$extra_data_dict.update({"index_ixx": str($i)})
47 #end if
48 #end for
49 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
50 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
51 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
52 #end if
53 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
54 $extra_data_dict)
55 #end if
56 <!-- Test with only the fasta file -->
4 <test> 57 <test>
5 <param name="genome_name" value="Dbia3"/> 58 <param name="genome_name" value="Dbia3"/>
6 <param name="fasta_file" value="common/dbia3.fa"/> 59 <param name="fasta_file" value="common/dbia3.fa"/>
7 <output name="output" file="only_genome/only_genome.html"> 60 <output name="output" file="only_genome/only_genome.html">
8 <!-- Use macro to check the whole common structure without repeated code --> 61 <!-- Use macro to check the whole common structure without repeated code -->
868 </extra_files> 921 </extra_files>
869 922
870 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> 923 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
871 </output> 924 </output>
872 </test> 925 </test>
873
874 <!-- Test TrixIndex for Blat alignment track -->
875 <test>
876 <param name="genome_name" value="Dbia3"/>
877 <param name="fasta_file" value="common/dbia3.fa"/>
878 <repeat name="group">
879 <param name="group_name" value="Default group"/>
880 <repeat name="format">
881 <conditional name="formatChoice">
882 <param name="format_select" value="bed" />
883 <conditional name="bedChoice">
884 <param name="bed_select" value="bed_blat_alignment_option"/>
885 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
886 <param name="longLabel" value="BLAT alignment" />
887 <param name="track_color" value="#000000"/>
888 <param name="database" value="NCBI" />
889 <conditional name="add_trix_index">
890 <param name="add_trix_index_selector" value="yes" />
891 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
892 </conditional>
893 </conditional>
894 </conditional>
895 </repeat>
896 </repeat>
897 <param name="debug_mode" value="true" />
898 <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
899 <extra_files type="file"
900 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
901 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
902 compare="sim_size"
903 />
904 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
905 <!-- check additional trackDb settings for BLAT -->
906 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
907 <assert_contents>
908 <has_text text="searchIndex"/>
909 <has_text text="searchTrix"/>
910 <has_text text="url"/>
911 <has_text text="urlLabel"/>
912 <has_text text="iframeUrl"/>
913 <has_text text="iframeOptions"/>
914 </assert_contents>
915 </extra_files>
916 <!-- check Trix index directory -->
917 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
918 value="trix_index/blat_out.ix" />
919 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
920 value="trix_index/blat_out.ixx" />
921 </output>
922 </test>
923
924 <!-- Test TrixIndex for BLAST Alignment -->
925 <test>
926 <param name="genome_name" value="Dbia3"/>
927 <param name="fasta_file" value="common/dbia3.fa"/>
928 <repeat name="group">
929 <param name="group_name" value="Default group"/>
930 <repeat name="format">
931 <conditional name="formatChoice">
932 <param name="format_select" value="bed" />
933 <conditional name="bedChoice">
934 <param name="bed_select" value="bed_blast_alignment_option"/>
935 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
936 <param name="longLabel" value="BLAST alignment" />
937 <param name="track_color" value="#000000"/>
938 <param name="database" value="NCBI" />
939 <conditional name="add_trix_index">
940 <param name="add_trix_index_selector" value="yes" />
941 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
942 </conditional>
943 </conditional>
944 </conditional>
945 </repeat>
946 </repeat>
947 <param name="debug_mode" value="true" />
948 <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
949 <extra_files type="file"
950 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
951 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
952 compare="sim_size"
953 />
954 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
955 <!-- check additional trackDb settings for BLAST -->
956 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
957 <assert_contents>
958 <has_text text="searchIndex"/>
959 <has_text text="searchTrix"/>
960 <has_text text="url"/>
961 <has_text text="urlLabel"/>
962 <has_text text="iframeUrl"/>
963 <has_text text="iframeOptions"/>
964 </assert_contents>
965 </extra_files>
966 <!-- check Trix index directory -->
967 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
968 value="trix_index/blast_out.ix" />
969 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
970 value="trix_index/blast_out.ixx" />
971 </output>
972 </test>
973
974 <!-- Test TrixIndex for BigBed -->
975 <test>
976 <param name="genome_name" value="Dbia3"/>
977 <param name="fasta_file" value="common/dbia3.fa"/>
978 <repeat name="group">
979 <param name="group_name" value="Default group"/>
980 <repeat name="format">
981 <conditional name="formatChoice">
982 <param name="format_select" value="bigbed"/>
983 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
984 <param name="longLabel" value="bigBed" />
985 <param name="track_color" value="#000000"/>
986 <conditional name="add_trix_index">
987 <param name="add_trix_index_selector" value="yes" />
988 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
989 <param name="trix_id" value="name" />
990 </conditional>
991 </conditional>
992 </repeat>
993 </repeat>
994 <param name="debug_mode" value="true" />
995 <output name="output" file="trix_index_files/bigbed_trackhub.html">
996 <extra_files type="file"
997 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
998 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
999 compare="sim_size"
1000 />
1001 <expand macro="verify_hub_structure" test="big_bed">
1002 <has_text text="searchIndex"/>
1003 <has_text text="searchTrix"/>
1004 </expand>
1005
1006 <!-- check Trix index directory -->
1007 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
1008 value="trix_index/blat_out.ix" />
1009 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
1010 value="trix_index/blat_out.ixx" />
1011 </output>
1012 </test>
1013
1014 <!-- Test for big files? -->
1015
1016 <!-- Find tests that should fail -->
1017 </xml>
1018 </macro>