Mercurial > repos > greg > ideas_preprocessor

changeset 31:c9f28cfea770 draft

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Uploaded
author greg
date Tue, 06 Feb 2018 09:33:18 -0500
parents 0cb6ff8ba6df
children ea739695619d
files ideas_preprocessor.xml test-data/IDEAS_input_config2.txt test-data/chromosomes2.bed test-data/output.html test-data/output2.html test-data/tmp.tar test-data/tmp.tar.gz test-data/tmp2.tar.gz
diffstat 8 files changed, 167 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_preprocessor.xml	Tue Feb 06 08:30:17 2018 -0500
+++ b/ideas_preprocessor.xml	Tue Feb 06 09:33:18 2018 -0500
@@ -161,6 +161,18 @@
                 <extra_files type="file" name="tmp.tar.gz" value="tmp.tar.gz" compare="sim_size"/>
             </output>
         </test>
+        <!--  This test requires a Galaxy instance configured with an hg19 chromosome length file.
+        <test>
+            <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
+            <param name="specify_chrom_windows" value="no"/>
+            <param name="window_size" value="50000000"/>
+            <output name="output" file="output2.html" ftype="ideaspre">
+                <extra_files type="file" name="chromosomes.bed" value="chromosomes2.bed"/>
+                <extra_files type="file" name="IDEAS_input_config.txt" value="IDEAS_input_config2.txt"/>
+                <extra_files type="file" name="tmp.tar.gz" value="tmp2.tar.gz" compare="sim_size"/>
+            </output>
+        </test>
+        -->
     </tests>
     <help>
 **What it does**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IDEAS_input_config2.txt	Tue Feb 06 09:33:18 2018 -0500
@@ -0,0 +1,1 @@
+e001 h3k4me3 tmp/e001-h3k4me3.bed.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chromosomes2.bed	Tue Feb 06 09:33:18 2018 -0500
@@ -0,0 +1,142 @@
+chr1	0	50000000
+chr1	50000000	100000000
+chr1	100000000	150000000
+chr1	150000000	200000000
+chr1	200000000	249250621
+chr2	0	50000000
+chr2	50000000	100000000
+chr2	100000000	150000000
+chr2	150000000	200000000
+chr2	200000000	243199373
+chr3	0	50000000
+chr3	50000000	100000000
+chr3	100000000	150000000
+chr3	150000000	198022430
+chr4	0	50000000
+chr4	50000000	100000000
+chr4	100000000	150000000
+chr4	150000000	191154276
+chr5	0	50000000
+chr5	50000000	100000000
+chr5	100000000	150000000
+chr5	150000000	180915260
+chr6	0	50000000
+chr6	50000000	100000000
+chr6	100000000	150000000
+chr6	150000000	171115067
+chr7	0	50000000
+chr7	50000000	100000000
+chr7	100000000	150000000
+chr7	150000000	159138663
+chrX	0	50000000
+chrX	50000000	100000000
+chrX	100000000	150000000
+chrX	150000000	155270560
+chr8	0	50000000
+chr8	50000000	100000000
+chr8	100000000	146364022
+chr9	0	50000000
+chr9	50000000	100000000
+chr9	100000000	141213431
+chr10	0	50000000
+chr10	50000000	100000000
+chr10	100000000	135534747
+chr11	0	50000000
+chr11	50000000	100000000
+chr11	100000000	135006516
+chr12	0	50000000
+chr12	50000000	100000000
+chr12	100000000	133851895
+chr13	0	50000000
+chr13	50000000	100000000
+chr13	100000000	115169878
+chr14	0	50000000
+chr14	50000000	100000000
+chr14	100000000	107349540
+chr15	0	50000000
+chr15	50000000	100000000
+chr15	100000000	102531392
+chr16	0	50000000
+chr16	50000000	90354753
+chr17	0	50000000
+chr17	50000000	81195210
+chr18	0	50000000
+chr18	50000000	78077248
+chr20	0	50000000
+chr20	50000000	63025520
+chrY	0	50000000
+chrY	50000000	59373566
+chr19	0	50000000
+chr19	50000000	59128983
+chr22	0	50000000
+chr22	50000000	51304566
+chr21	0	48129895
+chr6_ssto_hap7	0	4928567
+chr6_mcf_hap5	0	4833398
+chr6_cox_hap2	0	4795371
+chr6_mann_hap4	0	4683263
+chr6_apd_hap1	0	4622290
+chr6_qbl_hap6	0	4611984
+chr6_dbb_hap3	0	4610396
+chr17_ctg5_hap1	0	1680828
+chr4_ctg9_hap1	0	590426
+chr1_gl000192_random	0	547496
+chrUn_gl000225	0	211173
+chr4_gl000194_random	0	191469
+chr4_gl000193_random	0	189789
+chr9_gl000200_random	0	187035
+chrUn_gl000222	0	186861
+chrUn_gl000212	0	186858
+chr7_gl000195_random	0	182896
+chrUn_gl000223	0	180455
+chrUn_gl000224	0	179693
+chrUn_gl000219	0	179198
+chr17_gl000205_random	0	174588
+chrUn_gl000215	0	172545
+chrUn_gl000216	0	172294
+chrUn_gl000217	0	172149
+chr9_gl000199_random	0	169874
+chrUn_gl000211	0	166566
+chrUn_gl000213	0	164239
+chrUn_gl000220	0	161802
+chrUn_gl000218	0	161147
+chr19_gl000209_random	0	159169
+chrUn_gl000221	0	155397
+chrUn_gl000214	0	137718
+chrUn_gl000228	0	129120
+chrUn_gl000227	0	128374
+chr1_gl000191_random	0	106433
+chr19_gl000208_random	0	92689
+chr9_gl000198_random	0	90085
+chr17_gl000204_random	0	81310
+chrUn_gl000233	0	45941
+chrUn_gl000237	0	45867
+chrUn_gl000230	0	43691
+chrUn_gl000242	0	43523
+chrUn_gl000243	0	43341
+chrUn_gl000241	0	42152
+chrUn_gl000236	0	41934
+chrUn_gl000240	0	41933
+chr17_gl000206_random	0	41001
+chrUn_gl000232	0	40652
+chrUn_gl000234	0	40531
+chr11_gl000202_random	0	40103
+chrUn_gl000238	0	39939
+chrUn_gl000244	0	39929
+chrUn_gl000248	0	39786
+chr8_gl000196_random	0	38914
+chrUn_gl000249	0	38502
+chrUn_gl000246	0	38154
+chr17_gl000203_random	0	37498
+chr8_gl000197_random	0	37175
+chrUn_gl000245	0	36651
+chrUn_gl000247	0	36422
+chr9_gl000201_random	0	36148
+chrUn_gl000235	0	34474
+chrUn_gl000239	0	33824
+chr21_gl000210_random	0	27682
+chrUn_gl000231	0	27386
+chrUn_gl000229	0	19913
+chrM	0	16571
+chrUn_gl000226	0	15008
+chr18_gl000207_random	0	4262
--- a/test-data/output.html	Tue Feb 06 08:30:17 2018 -0500
+++ b/test-data/output.html	Tue Feb 06 09:33:18 2018 -0500
@@ -1,7 +1,8 @@
-<html><head></head><body><h3>Files prepared for IDEAS</h3>
+<html><head></head><body>
+<h3>Files prepared for IDEAS</h3>
 <ul>
 <li><a href="chromosome_windows.txt">chromosome_windows.txt</a></li>
+<li><a href="IDEAS_input_config.txt">IDEAS_input_config.txt</a></li>
+<li><a href="tmp.tar.gz">tmp.tar.gz</a></li>
 <li><a href="chromosomes.bed">chromosomes.bed</a></li>
-<li><a href="IDEAS_input_config.txt">IDEAS_input_config.txt</a></li>
-<li><a href="tmp.tar">tmp.tar</a></li>
-</ul></body></html>
\ No newline at end of file
+</ul></body></html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output2.html	Tue Feb 06 09:33:18 2018 -0500
@@ -0,0 +1,7 @@
+<html><head></head><body>
+<h3>Files prepared for IDEAS</h3>
+<ul>
+<li><a href="IDEAS_input_config.txt">IDEAS_input_config.txt</a></li>
+<li><a href="tmp.tar.gz">tmp.tar.gz</a></li>
+<li><a href="chromosomes.bed">chromosomes.bed</a></li>
+</ul></body></html>
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Binary file test-data/tmp.tar.gz has changed
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