Mercurial > repos > iuc > pysradb_search
changeset 2:b91e1e70f3a1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb commit 2d911e00c68a1be27d3627acd5020ee12378919b
| author | iuc |
|---|---|
| date | Mon, 23 Jan 2023 16:10:06 +0000 |
| parents | f63cf0adfd87 |
| children | |
| files | macros.xml pysradb.xml test-data/test_01.tabular test-data/test_01_histogram1.jpg test-data/test_01_histogram2.jpg test-data/test_01_histogram3.jpg test-data/test_01_stats.txt test-data/test_02_stats.txt test-data/test_03.txt test-data/test_04.txt test-data/test_05_stats.txt test-data/test_06_stats.txt |
| diffstat | 12 files changed, 35 insertions(+), 164 deletions(-) [+] |
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--- a/macros.xml Wed Nov 30 13:19:36 2022 +0000 +++ b/macros.xml Mon Jan 23 16:10:06 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.4.2</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@SUFFIX_VERSION@">2</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">pysradb</xref>
--- a/pysradb.xml Wed Nov 30 13:19:36 2022 +0000 +++ b/pysradb.xml Mon Jan 23 16:10:06 2023 +0000 @@ -13,9 +13,7 @@ #else --query '${query}' #end if - #if $conditional_mode.source - --source '${conditional_mode.source}' - #end if + --source '${conditional_mode.source}' #if $conditional_mode.selector == 'false' --organism '${conditional_mode.organism}' #end if @@ -28,7 +26,6 @@ #if $selection --selection '${selection}' #end if - --source $conditional_mode.source #if $strategy --strategy '${strategy}' #end if @@ -62,7 +59,7 @@ && gawk -F '\t' '{print $12}' 'output.tsv' | tail -n +2 | sort | uniq -c | gawk '{ print " ", $0 }' >> stats.txt #end if #end if - && echo $'\n Query keyworkds: ${query}\n' >> stats.txt + && echo $'\n Query keywords: ${query}\n' >> stats.txt #end if #if 'graphs' in $output_options.output_files && convert 'search_plots/Histogram*.svg' -set filename:fn '%[basename]' 'search_plots/%[filename:fn].jpg' @@ -288,12 +285,34 @@ <param name="max" value="100"/> <param name="output_files" value="stats,graphs"/> </section> - <output name="metadata_file" file="test_01.tabular" ftype="tsv"/> - <output name="stats" file="test_01_stats.txt" ftype="txt"/> + <output name="metadata_file" ftype="tsv"> + <assert_contents> + <has_n_lines n="101"/> + <has_n_columns n="16"/> + </assert_contents> + </output> + <output name="stats" ftype="txt"> + <assert_contents> + <has_text text="Statistics for the search query:"/> + <has_text text="Query keywords: cancer"/> + </assert_contents> + </output> <output_collection name="graphs_collection" type="list" count="3"> - <element name="histogram_base_count" file="test_01_histogram1.jpg" ftype="jpg" compare='sim_size'/> - <element name="histogram_library" file="test_01_histogram2.jpg" ftype="jpg" compare='sim_size'/> - <element name="histogram_publication" file="test_01_histogram3.jpg" ftype="jpg" compare='sim_size'/> + <element name="histogram_base_count" ftype="jpg"> + <assert_contents> + <has_size value="82507" delta="10000"/> + </assert_contents> + </element> + <element name="histogram_library" ftype="jpg"> + <assert_contents> + <has_size value="49925" delta="10000"/> + </assert_contents> + </element> + <element name="histogram_publication" ftype="jpg"> + <assert_contents> + <has_size value="46059" delta="10000"/> + </assert_contents> + </element> </output_collection> </test> <!-- Test 02: Specific search options-->
--- a/test-data/test_01.tabular Wed Nov 30 13:19:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -study_accession experiment_accession experiment_title sample_taxon_id sample_scientific_name experiment_library_strategy experiment_library_source experiment_library_selection sample_accession sample_alias experiment_instrument_model pool_member_spots run_1_size run_1_accession run_1_total_spots run_1_total_bases -SRP410072 SRX18392441 RNAseq of Homo Sapiens: gastric cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876555 LST1 NextSeq 550 38695273 345268738 SRR22422946 38695273 1916686097 -SRP410072 SRX18392440 RNAseq of Homo Sapiens: gastric cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876554 LET1 NextSeq 550 38939248 395787865 SRR22422947 38939248 1929190959 -SRP410072 SRX18392433 RNAseq of Homo Sapiens: colon cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876547 CC102 NextSeq 550 48692092 725233955 SRR22422954 48692092 3672865478 -SRP410072 SRX18392432 RNAseq of Homo Sapiens: colon cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876546 CC86 NextSeq 550 35645786 487240987 SRR22422955 35645786 1766620685 -SRP410072 SRX18392431 RNAseq of Homo Sapiens: urothelial cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876545 BLC1 NextSeq 550 21446733 183106366 SRR22422956 21446733 1059212738 -SRP410072 SRX18392430 RNAseq of Homo Sapiens: colon cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876544 CC89 NextSeq 550 30244954 351063682 SRR22422957 30244954 1497301752 -SRP410072 SRX18392429 RNAseq of Homo Sapiens: colon cancer 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15876543 CC76 NextSeq 550 30955620 355418256 SRR22422958 30955620 1532890915 -SRP409548 SRX18369025 GSM6755011: BT474.F.hand.72hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855457 GSM6755011 Illumina NovaSeq 6000 54657341 2488903938 SRR22399318 27449042 7451954013 -SRP409548 SRX18369024 GSM6755010: BT474.E.print.72hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855456 GSM6755010 Illumina NovaSeq 6000 40290093 1817229960 SRR22399320 20231478 5498476460 -SRP409548 SRX18369023 GSM6755009: BT474.D.hand.24hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855455 GSM6755009 Illumina NovaSeq 6000 37645842 1686613884 SRR22399322 18895035 5064959758 -SRP409548 SRX18369022 GSM6755008: BT474.C.print.24hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855454 GSM6755008 Illumina NovaSeq 6000 42730064 1951990096 SRR22399324 21430063 5838220284 -SRP409548 SRX18369021 GSM6755007: BT474.B.hand.1hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855453 GSM6755007 Illumina NovaSeq 6000 64955526 2982091712 SRR22399326 32607072 8881051651 -SRP409548 SRX18369020 GSM6755006: BT474.A.print.1hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855452 GSM6755006 Illumina NovaSeq 6000 30138739 1292900468 SRR22399328 15153574 3950782486 -SRP409548 SRX18369019 GSM6755005: MCF7.F.hand.72hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855451 GSM6755005 Illumina NovaSeq 6000 58927255 2623809213 SRR22399330 29594180 7893390358 -SRP409548 SRX18369018 GSM6755004: MCF7.E.print.72hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855450 GSM6755004 Illumina NovaSeq 6000 48925847 2232507875 SRR22399332 24576417 6746264388 -SRP409548 SRX18369017 GSM6755003: MCF7.D.hand.24hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855449 GSM6755003 Illumina NovaSeq 6000 38694756 1742096832 SRR22399334 19397787 5207165461 -SRP409548 SRX18369016 GSM6755002: MCF7.C.print.24hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855448 GSM6755002 Illumina NovaSeq 6000 40416603 1814017558 SRR22399336 20295472 5427103600 -SRP409548 SRX18369015 GSM6755001: MCF7.B.hand.1.hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855447 GSM6755001 Illumina NovaSeq 6000 29613366 1342195585 SRR22399338 14897585 4009554602 -SRP409548 SRX18369014 GSM6755000: MCF7.A.print.1hr; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15855446 GSM6755000 Illumina NovaSeq 6000 40661730 1837853357 SRR22399340 20413083 5559364008 -SRP408991 SRX18330342 GSM6745556: MDA-MB-231 cells, OE-YWHAB; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15819529 GSM6745556 Illumina NovaSeq 6000 23077362 2244316187 SRR22359478 23077362 6923208600 -SRP408991 SRX18330341 GSM6745555: MDA-MB-231 cells, Vector Control; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15819528 GSM6745555 Illumina NovaSeq 6000 20900395 2047201792 SRR22359479 20900395 6270118500 -SRP408888 SRX18326041 GSM6744353: MDAMB231 cells, siRNF31-3; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815406 GSM6744353 Illumina HiSeq 2500 23829209 1004163155 SRR22355074 23829209 1191460450 -SRP408888 SRX18326040 GSM6744352: MDAMB231 cells, siRNF31-2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815405 GSM6744352 Illumina HiSeq 2500 23846123 995457257 SRR22355075 23846123 1192306150 -SRP408888 SRX18326039 GSM6744351: MDAMB231 cells, siRNF31-1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815403 GSM6744351 Illumina HiSeq 2500 23847447 996527320 SRR22355076 23847447 1192372350 -SRP408888 SRX18326038 GSM6744350: MDAMB231 cells, siControl-3; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815402 GSM6744350 Illumina HiSeq 2500 23836238 996486446 SRR22355077 23836238 1191811900 -SRP408888 SRX18326037 GSM6744349: MDAMB231 cells, siControl-2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815404 GSM6744349 Illumina HiSeq 2500 23852614 998645972 SRR22355078 23852614 1192630700 -SRP408888 SRX18326036 GSM6744348: MDAMB231 cells, siControl-1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15815401 GSM6744348 Illumina HiSeq 2500 23827102 995610104 SRR22355079 23827102 1191355100 -SRP408833 SRX18323238 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813268 P39 Illumina NovaSeq 6000 25341979 2513178560 SRR22352265 25341979 7602593700 -SRP408833 SRX18323237 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813267 P30 Illumina NovaSeq 6000 21776549 2141796872 SRR22352266 21776549 6532964700 -SRP408833 SRX18323236 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813266 P24 Illumina NovaSeq 6000 21643539 2157913695 SRR22352267 21643539 6493061700 -SRP408833 SRX18323235 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813265 P7 Illumina NovaSeq 6000 20460130 2045597710 SRR22352268 20460130 6138039000 -SRP408833 SRX18323234 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813264 P9 Illumina NovaSeq 6000 21406005 2055388382 SRR22352269 21406005 6421801500 -SRP408833 SRX18323233 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813263 P5 Illumina NovaSeq 6000 24128081 2356284512 SRR22352270 24128081 7238424300 -SRP408833 SRX18323232 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813262 P4 Illumina NovaSeq 6000 22323001 2387187610 SRR22352271 22323001 6696900300 -SRP408833 SRX18323231 RNA-Seq of Homo sapiens CRC organoid 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15813261 P1 Illumina NovaSeq 6000 23801340 2330724568 SRR22352272 23801340 7140402000 -ERP021251 ERX1877814 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532455 SAMEA70755418 Illumina HiSeq 2000 14439188 1984175679 ERR1815302 14439188 2887837600 -ERP021251 ERX1877815 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532456 SAMEA70756168 Illumina HiSeq 2000 12679859 1748831662 ERR1815303 12679859 2535971800 -ERP021251 ERX1877813 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532454 SAMEA70754668 Illumina HiSeq 2000 10272804 1406223913 ERR1815301 10272804 2054560800 -ERP021251 ERX1877812 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532453 SAMEA70753918 Illumina HiSeq 2000 11611497 1588179875 ERR1815300 11611497 2322299400 -ERP021251 ERX1877811 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532452 SAMEA70753168 Illumina HiSeq 2000 14052584 1919296954 ERR1815299 14052584 2810516800 -ERP021251 ERX1877810 Illumina HiSeq 2000 paired end sequencing; Muscle to cancer crosstalk: Myokines released from contracting myotubes of postmenopausal women reduce breast cancer cell growth 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC Inverse rRNA ERS1532451 SAMEA70752418 Illumina HiSeq 2000 14039766 1925115500 ERR1815298 14039766 2807953200 -SRP408494 SRX18299494 GSM6738160: 6-2PA1_NP_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790461 GSM6738160 Illumina NovaSeq 6000 44587439 2895345355 SRR22326455 44587439 9006662678 -SRP408494 SRX18299493 GSM6738159: 6PA1_NP_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790460 GSM6738159 Illumina NovaSeq 6000 36436891 2331543805 SRR22326456 36436891 7360251982 -SRP408494 SRX18299492 GSM6738158: 5-2PA1_TAP_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790459 GSM6738158 Illumina NovaSeq 6000 41868418 2684881937 SRR22326457 41868418 8457420436 -SRP408494 SRX18299491 GSM6738157: 5PA1_TAP_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790458 GSM6738157 Illumina NovaSeq 6000 44466023 2836877395 SRR22326458 44466023 8982136646 -SRP408494 SRX18299490 GSM6738156: 4-2PA1_Mock_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790457 GSM6738156 Illumina NovaSeq 6000 44730889 2864467864 SRR22326459 44730889 9035639578 -SRP408494 SRX18299489 GSM6738155: 4PA1_Mock_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790456 GSM6738155 Illumina NovaSeq 6000 38409511 2455052059 SRR22326460 38409511 7758721222 -SRP408494 SRX18299488 GSM6738154: 3-2AS1_NP_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790455 GSM6738154 Illumina NovaSeq 6000 40198418 2581416299 SRR22326461 40198418 8120080436 -SRP408494 SRX18299487 GSM6738153: 3AS1_NP_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790454 GSM6738153 Illumina NovaSeq 6000 41345661 2647677421 SRR22326462 41345661 8351823522 -SRP408494 SRX18299486 GSM6738152: 2-2AS1_TAP_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790453 GSM6738152 Illumina NovaSeq 6000 39858247 2551705751 SRR22326463 39858247 8051365894 -SRP408494 SRX18299485 GSM6738151: 2AS1_TAP_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790452 GSM6738151 Illumina NovaSeq 6000 39192401 2514153484 SRR22326464 39192401 7916865002 -SRP408494 SRX18299484 GSM6738150: 1-2AS1_Mock_n2; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790451 GSM6738150 Illumina NovaSeq 6000 41100992 2610855889 SRR22326465 41100992 8302400384 -SRP408494 SRX18299483 GSM6738149: 1AS1_Mock_n1; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15790450 GSM6738149 Illumina NovaSeq 6000 34455185 2210877656 SRR22326466 34455185 6959947370 -SRP408485 SRX18298790 GSM6738033: Hashtagged_scVDJ_sample_2; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15789759 GSM6738033 Illumina NovaSeq 6000 21390946 3232595879 SRR22325731 21390946 9861226106 -SRP408485 SRX18298789 GSM6738032: Hashtagged_scVDJ_sample_1; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15789758 GSM6738032 Illumina NovaSeq 6000 21075444 3180834816 SRR22325732 21075444 9715779684 -SRP408403 SRX18292849 GSM6736158: RC_j; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784263 GSM6736158 Illumina MiSeq 14681222 4082806845 SRR22319585 14681222 7369973444 -SRP408403 SRX18292848 GSM6736157: RC_i; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784262 GSM6736157 Illumina MiSeq 13774413 3977557176 SRR22319586 13774413 6914755326 -SRP408403 SRX18292847 GSM6736156: RC_h; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784261 GSM6736156 Illumina MiSeq 14043696 4110521736 SRR22319587 14043696 7049935392 -SRP408403 SRX18292846 GSM6736155: RC_g; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784260 GSM6736155 Illumina MiSeq 12192519 3316867161 SRR22319588 12192519 6120644538 -SRP408403 SRX18292845 GSM6736154: RC_f; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784259 GSM6736154 Illumina MiSeq 14455270 4035467899 SRR22319589 14455270 7256545540 -SRP408403 SRX18292844 GSM6736153: RC_e; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784258 GSM6736153 Illumina MiSeq 12983855 3293183917 SRR22319590 12983855 6517895210 -SRP408403 SRX18292843 GSM6736152: RC_d; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784257 GSM6736152 Illumina MiSeq 11509633 3083082225 SRR22319591 11509633 5777835766 -SRP408403 SRX18292842 GSM6736151: RC_c; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784256 GSM6736151 Illumina MiSeq 12885539 3512469452 SRR22319592 12885539 6468540578 -SRP408403 SRX18292841 GSM6736150: RC_b; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784255 GSM6736150 Illumina MiSeq 11139511 2765032112 SRR22319593 11139511 5592034522 -SRP408403 SRX18292840 GSM6736149: RC_a; Homo sapiens; OTHER 9606 Homo sapiens OTHER TRANSCRIPTOMIC other SRS15784254 GSM6736149 Illumina MiSeq 12321401 3260439508 SRR22319594 12321401 6185343302 -SRP408275 SRX18287695 GSM6735086: Sample_Anaerobic_CRS_006_A09; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779451 GSM6735086 Illumina NovaSeq 6000 29085510 2626384710 SRR22314242 29085510 8783824020 -SRP408275 SRX18287694 GSM6735085: Sample_Anaerobic_CRS_006_A08; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779450 GSM6735085 Illumina NovaSeq 6000 29039377 2615837661 SRR22314243 29039377 8769891854 -SRP408275 SRX18287693 GSM6735084: Sample_Anaerobic_CRS_005_A09; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779449 GSM6735084 Illumina NovaSeq 6000 33863103 3052764520 SRR22314244 33863103 10226657106 -SRP408275 SRX18287692 GSM6735083: Sample_Anaerobic_CRS_005_A08; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779448 GSM6735083 Illumina NovaSeq 6000 28545795 2583781182 SRR22314245 28545795 8620830090 -SRP408275 SRX18287691 GSM6735082: Sample_Anaerobic_CRS_005_A07; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779447 GSM6735082 Illumina NovaSeq 6000 27744898 2498417257 SRR22314246 27744898 8378959196 -SRP408275 SRX18287690 GSM6735081: Sample_Anaerobic_006_A07; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779446 GSM6735081 Illumina NovaSeq 6000 25736047 2332319317 SRR22314247 25736047 7772286194 -SRP408275 SRX18287689 GSM6735080: Sample_Anaerobic_006_A06; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779445 GSM6735080 Illumina NovaSeq 6000 28977475 2650126292 SRR22314248 28977475 8751197450 -SRP408275 SRX18287688 GSM6735079: Sample_Anaerobic_006_A05; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779444 GSM6735079 Illumina NovaSeq 6000 31369992 2825445760 SRR22314249 31369992 9473737584 -SRP408275 SRX18287687 GSM6735078: Sample_Anaerobic_006_A04; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779443 GSM6735078 Illumina NovaSeq 6000 28725226 2604615760 SRR22314250 28725226 8675018252 -SRP408275 SRX18287686 GSM6735077: Sample_Anaerobic_006_A03; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779442 GSM6735077 Illumina NovaSeq 6000 27883463 2530016685 SRR22314251 27883463 8420805826 -SRP408275 SRX18287685 GSM6735076: Sample_Anaerobic; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779441 GSM6735076 Illumina NovaSeq 6000 26941491 2448949773 SRR22314252 26941491 8136330282 -SRP408275 SRX18287684 GSM6735075: Sample_Aerobic_006_A02; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779440 GSM6735075 Illumina NovaSeq 6000 27791914 2504363853 SRR22314253 27791914 8393158028 -SRP408275 SRX18287683 GSM6735074: Sample_Aerobic_006_A01; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779439 GSM6735074 Illumina NovaSeq 6000 28427058 2558553956 SRR22314254 28427058 8584971516 -SRP408275 SRX18287682 GSM6735073: Sample_Aerobic_005_A03; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779438 GSM6735073 Illumina NovaSeq 6000 25802689 2341335991 SRR22314255 25802689 7792412078 -SRP408275 SRX18287681 GSM6735072: Sample_Aerobic_005_A02; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779437 GSM6735072 Illumina NovaSeq 6000 31207884 2843313856 SRR22314256 31207884 9424780968 -SRP408275 SRX18287680 GSM6735071: Sample_Aerobic_005_A01; Homo sapiens; RNA-Seq 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC cDNA SRS15779436 GSM6735071 Illumina NovaSeq 6000 24557588 2225432236 SRR22314257 24557588 7416391576 -SRP296872 SRX18280591 HupT4_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772928 HupT4_2 Illumina HiSeq 4000 5757600 287084861 SRR22306978 5757600 568280566 -SRP296872 SRX18280590 HupT4_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772927 HupT4_1 Illumina HiSeq 4000 5300331 265525417 SRR22306979 5300331 524458844 -SRP296872 SRX18280589 Hs766T_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772926 Hs766T_2 Illumina HiSeq 4000 3377702 170354914 SRR22306980 3377702 335016432 -SRP296872 SRX18280588 Hs766T_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772925 Hs766T_1 Illumina HiSeq 4000 5519712 279392682 SRR22306981 5519712 547325469 -SRP296872 SRX18280587 CAPAN2_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772924 CAPAN2_2 Illumina HiSeq 4000 5381543 269083199 SRR22306982 5381543 533076966 -SRP296872 SRX18280586 CAPAN2_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772923 CAPAN2_1 Illumina HiSeq 4000 4201648 209428495 SRR22306983 4201648 416162878 -SRP296872 SRX18280585 MIAPaCa2_HNRNPF_SEdel_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772922 MIAPaCa2_HNRNPF_SEdel_2 Illumina HiSeq 4000 28231792 706274390 SRR22306984 28231792 2117384400 -SRP296872 SRX18280584 MIAPaCa2_HNRNPF_SEdel_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772921 MIAPaCa2_HNRNPF_SEdel_1 Illumina HiSeq 4000 29933403 748854658 SRR22306985 29933403 2245005225 -SRP296872 SRX18280583 MIAPaca2_Parental_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772920 MIAPaca2_Parental_2 Illumina HiSeq 4000 31077260 767261609 SRR22306986 31077260 2330794500 -SRP296872 SRX18280582 MIAPaca2_Parental_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772919 MIAPaca2_Parental_1 Illumina HiSeq 4000 30578371 759273365 SRR22306987 30578371 2293377825 -SRP296872 SRX18280581 MIAPaCa2_HNRNPF_KO5_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772918 MIAPaCa2_HNRNPF_KO5_2 Illumina HiSeq 4000 17526074 550031747 SRR22306988 17526074 1733705702 -SRP296872 SRX18280580 MIAPaCa2_HNRNPF_KO5_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772917 MIAPaCa2_HNRNPF_KO5_1 Illumina HiSeq 4000 14512269 455410832 SRR22306989 14512269 1445978757 -SRP296872 SRX18280579 MIAPaca2_WT_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772916 MIAPaca2_WT_2 Illumina HiSeq 4000 19251676 601142916 SRR22306990 19251676 1918361956 -SRP296872 SRX18280578 MIAPaca2_WT_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772915 MIAPaca2_WT_1 Illumina HiSeq 4000 18294850 572389714 SRR22306991 18294850 1816322930 -SRP296872 SRX18280577 YAPC_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772914 YAPC_2 Illumina HiSeq 4000 5832937 291586955 SRR22306992 5832937 578923280 -SRP296872 SRX18280576 YAPC_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772913 YAPC_1 Illumina HiSeq 4000 9511112 475803185 SRR22306993 9511112 943419455 -SRP296872 SRX18280575 CAPAN1_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772912 CAPAN1_2 Illumina HiSeq 4000 7161336 360000653 SRR22306994 7161336 709587782 -SRP296872 SRX18280574 Su8686_2 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772910 Su8686_2 Illumina HiSeq 4000 5237585 263155000 SRR22306995 5237585 517956746 -SRP296872 SRX18280573 Su8686_1 9606 Homo sapiens RNA-Seq TRANSCRIPTOMIC RANDOM SRS15772911 Su8686_1 Illumina HiSeq 4000 5686219 284393282 SRR22306996 5686219 563282085
--- a/test-data/test_01_stats.txt Wed Nov 30 13:19:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - - Statistics for the search query: - ================================= - Number of unique studies: 11 - Number of unique experiments: 100 - Number of unique runs: 112 - Number of unique samples: 100 - Mean base count of samples: 5256601253.884 - Median base count of samples: 5979432411.000 - Sample base count standard deviation: 2991739423.009 - Date range: - 2022-11: 100 - - Organisms: - Homo sapiens: 100 - - Platform: - ILLUMINA: 100 - - Library strategy: - OTHER: 12 - RNA-Seq: 88 - - Library source: - TRANSCRIPTOMIC: 100 - - Library selection: - Inverse rRNA: 6 - RANDOM: 19 - cDNA: 63 - other: 12 - - Library layout: - PAIRED: 68 - SINGLE: 32 - - - Sequencing instrument: - 6 Illumina HiSeq 2000 - 6 Illumina HiSeq 2500 - 19 Illumina HiSeq 4000 - 10 Illumina MiSeq - 52 Illumina NovaSeq 6000 - 7 NextSeq 550 - - Query keyworkds: cancer -
--- a/test-data/test_02_stats.txt Wed Nov 30 13:19:36 2022 +0000 +++ b/test-data/test_02_stats.txt Mon Jan 23 16:10:06 2023 +0000 @@ -33,5 +33,5 @@ Sequencing instrument: 1 Illumina NovaSeq 6000 - Query keyworkds: + Query keywords:
--- a/test-data/test_03.txt Wed Nov 30 13:19:36 2022 +0000 +++ b/test-data/test_03.txt Mon Jan 23 16:10:06 2023 +0000 @@ -32,5 +32,5 @@ - Query keyworkds: cancer + Query keywords: cancer
--- a/test-data/test_04.txt Wed Nov 30 13:19:36 2022 +0000 +++ b/test-data/test_04.txt Mon Jan 23 16:10:06 2023 +0000 @@ -61,5 +61,5 @@ 11 Illumina MiSeq 1 NextSeq 500 - Query keyworkds: escherichia + Query keywords: escherichia