| Next changeset 1:02831bf9e95f (2021-05-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679" |
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added:
pretext_map.xml test-data/fullmap1.jpg test-data/fullmap2.bmp test-data/map.pretext test-data/output_1.pretext test-data/output_2.pretext test-data/output_3.pretext test-data/snapshot1.jpg test-data/snapshot2.jpg test-data/snapshot3.jpg test-data/test.bam test-data/test.sam |
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| diff -r 000000000000 -r 7c2e9bc2123b pretext_map.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pretext_map.xml Wed May 05 15:09:54 2021 +0000 |
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| @@ -0,0 +1,132 @@ +<tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <macros> + <token name="@TOOL_VERSION@">0.1.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement> + <requirement type="package" version="1.12">samtools</requirement> + </requirements> + <version_command>PretextMap --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + #if $input.is_of_type("bam"): + samtools view -h '${input}' | + #else + cat '${input}' | + #end if + PretextMap + #if $sorting.sortby == "length": + --sortby length + --sortorder $sorting.sortorder + #elif $sorting.sortby == "name": + --sortby name + --sortorder $sorting.sortorder + #end if + #if $map_qual: + --mapq $map_qual + #end if + #if $filter.filter_type == "in": + --filterInclude '$filter.filter_list' + #elif $filter.filter_type == "out": + --filterExclude '$filter.filter_list' + #end if + -o output.pretext + ]]></command> + <inputs> + <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/> + <conditional name="sorting"> + <param argument="--sortby" type="select" label="Sort by"> + <option value="nosort" selected="true">Don't sort</option> + <option value="length">Length</option> + <option value="name">Name</option> + </param> + <when value="nosort"/> + <when value="length"> + <param argument="--sortorder" type="select" label="Sort order: "> + <option value="ascend">Ascending</option> + <option value="decend">Decending</option> + </param> + </when> + <when value="name"> + <param argument="--sortorder" type="select" label="Sort order: "> + <option value="ascend">Ascending</option> + <option value="descend">Decending</option> + </param> + </when> + </conditional> + <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/> + <conditional name="filter"> + <param name="filter_type" type="select" label="How to filter: "> + <option value="" selected="true">No filter</option> + <option value="in">Filter to include only specified sequence names</option> + <option value="out">Filter to exclude specified sequence names</option> + </param> + <when value=""/> + <when value="in"> + <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + </when> + <when value="out"> + <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input" ftype="bam" value="test.bam"/> + <conditional name="sorting"> + <param name="sortby" value="length"/> + <param name="sortorder" value="ascend"/> + </conditional> + <conditional name="filter"> + <param name="filter_type" value="in"/> + <param name="filter_list" value="ref"/> + </conditional> + <param name="map_qual" value="10"/> + <output name="pretext_map_out" file="output_1.pretext"/> + </test> + <test> + <param name="input" ftype="sam" value="test.sam"/> + <conditional name="sorting"> + <param name="sortby" value="name"/> + <param name="sortorder" value="descend"/> + </conditional> + <conditional name="filter"> + <param name="filter_type" value="out"/> + <param name="filter_list" value="chrM, chr8, chr9"/> + </conditional> + <output name="pretext_map_out" file="output_2.pretext"/> + </test> + </tests> + <help><![CDATA[ + +**What is does** + +The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps. +Pretext has no special requirement on the alignment files +process your alignments however you want before feeding to PretextMap. + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{Harry_et_al, + Author={Harry, E}, + title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.}, + url = {https://github.com/wtsi-hpag/PretextSnapshot},} + </citation> + </citations> +</tool> |
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| b'@@ -0,0 +1,100 @@\n+HWI-EAS269B:8:34:797:623\t145\tchr1\t16632182\t255\t27M\t=\t16631977\t0\tCCATTTCCTGTATGCTGTAAAGTACAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:40:39:1184\t145\tchr1\t24620331\t3\t27M\t=\t24620115\t0\tATTTATGTGGTTTCGTTTACCTTCTAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chrM\tCP:i:9060\n+HWI-EAS269B:8:58:533:1198\t81\tchr1\t88426079\t255\t27M\t=\t88423429\t0\tGAAGAGGAAGAAGGTGGGGAGGAAGAG\tIIIG?IIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:89:1776:1815\t97\tchr1\t134085638\t255\t27M\t=\t134085824\t0\tGAATGATTCTCTGGGTGTTACTTTGCA\tIIIIIIIIIIIIIIIDIII:IIII>F5\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:74:1134:1670\t161\tchr1\t138166886\t255\t27M\t=\t138167084\t0\tTTACTAGTGTCTCTCTTACCATCATAT\t.IIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:59:1321:1427\t147\tchr1\t173149715\t255\t27M\t=\t173149555\t0\tAAGGGCTAGGGTGACAGGCAGGGGACG\t-C<CID?IIIIIIIDIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:8:164:1678\t145\tchr1\t178660716\t255\t27M\t=\t178660493\t0\tCAATTGGTGTTTTTCTTAAGAGACTCA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:1:1048:638\t137\tchr10\t12456478\t1\t27M\t*\t0\t0\tTAAAANAAATAAAACAAAACAATAAAA\t$\'&(+")\'%$(&*&#&$$#%%$$%%$$\tNM:i:2\tNH:i:4\tCC:Z:chr16\tCP:i:21639623\n+HWI-EAS269:3:62:1211:798\t147\tchr10\t28135294\t255\t27M\t=\t28135117\t0\tACATGGTGTGGGGACAGAGATGTGAAG\tI;IIIIIIAIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:27:410:424\t145\tchr10\t76950070\t255\t27M\t=\t76949871\t0\tGAGTCTGTGTCCAGGCCAATTCACTAT\t25-8I+.6B.IIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:48:1180:1122\t73\tchr10\t83772157\t0\t27M\t*\t0\t0\tGATCATCTTTTCTAAAACAATAAAGAC\t/IIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:6\tCC:Z:chr11\tCP:i:93811140\n+HWI-EAS269:3:77:654:131\t99\tchr10\t93419810\t255\t27M\t=\t93419993\t0\tTTGCATCCCTAGGAACTGGAGTTATAG\tIIIIIIGIHIIIED@CIIH5I3D9G6:\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:98:895:1810\t177\tchr11\t3371472\t255\t27M\t=\t37952212\t0\tCTACATAGTGGGAACCGGCGACCGCTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:2\tNH:i:1\n+HWI-EAS269B:8:58:1126:883\t97\tchr11\t30080486\t255\t27M\t=\t30080702\t0\tTACTTCCACCAGGCTCCAGTTTTGTGA\tIIIIIIIIIIIIIIIIIIIIIIIIII5\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:89:1763:1446\t81\tchr11\t59589605\t255\t27M\t=\t59589400\t0\tGTACCTGGCCACTGATGCAGCTTAGAA\tII<IIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:6:739:1329\t161\tchr11\t68629628\t3\t27M\t=\t68629835\t0\tGTTTTTGGTTGATAGTTGAGCAAACTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chr4\tCP:i:126661877\n+HWI-EAS269:3:19:1683:1350\t81\tchr11\t70846915\t255\t27M\t=\t70846725\t0\tCACGGGCAGATAAGCTGCTGAGACTAA\tH50BB:IF=IIGIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:9:1691:1087\t97\tchr11\t84640783\t255\t27M\t=\t84641010\t0\tACATTATCCATCTCTCTGTCATTGTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:48:1350:424\t81\tchr11\t94150331\t255\t27M\t=\t94150113\t0\tTTGCAAGCCAACCCTGAGTGAAGTGTC\tIIDHIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:22:1176:1405\t97\tchr11\t98629843\t255\t27M\t=\t98630030\t0\tCCCTCGGAGGGCAACGGGAAAGGAGAA\tIIIIIIIIIIIDIIIII?III/79E14\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:67:1311:1512\t97\tchr11\t100488190\t255\t27M\t=\t100488374\t0\tCATGCCCTGAGACTTAGCAAGACTCTT\tIIIIIIIIIIIIIIIEIA3,I57GBI@\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:41:1142:1307\t161\tchr11\t101320424\t255\t27M\t=\t101320625\t0\tGCCTCCCTACATAGCAAAGGAAAGAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:31:1101:21\t97\tchr11\t116711287\t255\t27M\t=\t116711485\t0\tCATAAGCAAAAGATACACCATGTTTTA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:84:637:1203\t145\tchr12\t35829424\t255\t27M\t=\t35829229\t0\tCTCCCTCAAGGATCTTGTGGGGCATCA\t</\'>I,I5B26$II;EB=%IIII1III\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:65:1158:1081\t163\tchr12\t52234332\t255\t27M\t=\t52234505\t0\tTTTTTTTTTTAAGACAGGGAGTTTTTT\tIIIIIIIIIIIC4,,*>II%-,%III>\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:65:1325:1287\t137\tchr12\t52234513\t3\t27M\t*\t0\t0\tGCAGCACCTTGTGACATTTAATTTAGT\tIIIII+IIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chr15\tCP:i:98780443\n+HWI-EAS269:3:38:488:1093\t97\tchr12\t80471642\t255\t27M\t=\t80471839\t0\tTGGAGAGATGACTCCTTGTTTGAGACA\tIIIIIIIIIIIIIIIIIIIBAE0B<7D\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:76:290:1451\t99\tchr12\t117745566\t0\t27M\t=\t117745739\t0\tCAATCTGAAGATCCACAATCTTTTATA\tIIIIIIIIIIIIIIFII5I9IIII+I7\tNM:i:0\tNH:i:5\tCC:Z:chr4\tCP:i:133520935\n+HWI-EAS269B:8:39:353:1526\t65\tchr13\t18122558\t255\t2'..b":1\n+HWI-EAS269B:8:13:280:189\t161\tchr7\t29184615\t255\t27M\t=\t29184814\t0\tCTTTTCCAACAGCGAGAAAAATGTACA\tIIIIIIIIIIIIIIIIIIIIIIIIDII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:19:72:273\t137\tchr7\t52258521\t255\t27M\t*\t0\t0\tATCAGAGGCACAGGGACAGGGTAAGGA\t&&2IIIII;E(IIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:40:235:869\t161\tchr7\t52631974\t255\t27M\t=\t52632179\t0\tGGCGCTGACTCCATCAGATATCCATTC\tIIIIIII7IIIIIII6IIIIIIIBIII\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:18:304:346\t129\tchr7\t107789557\t255\t27M\t=\t33158390\t0\tCACGTACTGTCACCTTGTAACATTTGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIF\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:3:698:297\t161\tchr7\t110976065\t255\t27M\t=\t110976385\t0\tGCAGTTATCACTTTCTTGCCATGGGCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:50:1269:965\t145\tchr7\t118217605\t255\t27M\t=\t118216239\t0\tACCTGTAGATCCACATGATCATGAAGA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:38:1381:1429\t83\tchr7\t136141344\t255\t27M\t=\t136141280\t0\tATCTGAAGTATCCCACATGTTGAGCTC\t<III@IIIIIIIII>IIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:25:781:386\t83\tchr8\t29844005\t255\t27M\t=\t29843841\t0\tTAAGGGAGGAAAGTGTTTCAGAGTGTA\t;83<159<<III@IIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:25:979:679\t163\tchr8\t72664237\t255\t27M\t=\t72664413\t0\tCTGATGGGAGCCCTGCGTGGTAAGAGG\tIIIIIIIIIII=III@I(II$27I>I4\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:23:1069:816\t145\tchr8\t74704433\t255\t27M\t=\t74704222\t0\tTGTTCTCAGTTGTGGACAAGTGACAGC\tI<GII@IIIIIIII;IIIIIIIIII0I\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:34:435:1679\t73\tchr8\t87366211\t3\t27M\t*\t0\t0\tAAGCCTAGGGCTTCTCCTCTACACCCC\tI556I;FCAIIIFI<IIIIIIIIIIII\tNM:i:0\tNH:i:2\n+HWI-EAS269B:8:32:1486:294\t97\tchr8\t124121215\t255\t27M\t=\t124121411\t0\tTGTTACCATACGCCCTTCTGCTGAGGC\tIIIIIIIIIIIIIIIIIIDIIIIGIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:32:142:1471\t81\tchr8\t124496752\t3\t27M\t=\t124496536\t0\tGGATCTGCTTCATGAGTTGCCACATTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:2\n+HWI-EAS269B:8:60:82:1806\t97\tchr8\t125945215\t255\t27M\t=\t125945423\t0\tAGATGCTGGCCATCCAGAGTAAGAACA\tIIIIIIIIIIIIIIIIIIIHIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:16:1162:495\t81\tchr8\t125945584\t255\t27M\t=\t125945381\t0\tGTTGCTCGCAGCTGGGGTGTGGGGCCA\t<CIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:1:165:1889\t81\tchr8\t126016885\t255\t27M\t=\t126016469\t0\tTGAGCAGGAAAACACTTTAAACCAGAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:66:939:1154\t145\tchr9\t17537149\t255\t27M\t=\t17536959\t0\tCTCCTTCAAGTACGCCTGGGTCTTAGA\tIDIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:68:1189:285\t81\tchr9\t61249807\t255\t27M\t=\t61242460\t0\tAGTCAAGCTCACTTGGCGGTGAAGGAT\t@.0;;A,?-F5I;7IIIIGIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:15:784:1754\t163\tchr9\t74846937\t255\t27M\t=\t74847108\t0\tGCACAGCACTGAGGAAAGGATCATCTC\tIIIIIIIIIIIIIIIIIIGII1CI7II\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:26:126:1382\t145\tchrM\t3413\t255\t27M\t=\t3190\t0\tGTTATTCTTTATAGCAGAGTACACTAA\tIIII8IB328I9IIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:90:320:1336\t73\tchrM\t6326\t255\t27M\t*\t0\t0\tATGATCTCCAGCTATCCTATGAGCCTT\tIIIIIIIIA.ICI.4'(=,C>7-*&@8\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:23:469:1215\t161\tchrM\t7472\t3\t27M\t=\t7676\t0\tATTTCATCTGAAGACGTCCTCCACTCA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:73:36:783\t161\tchrM\t7958\t3\t27M\t=\t8152\t0\tCCCCAACAATAATAGGATTCCCAATCG\tIIIIIIIIIIIIIIIIIIIII09I>>I\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:33:1528:954\t99\tchrM\t8012\t3\t27M\t=\t8186\t0\tTCCTATTCCCATCCTCAAAACGCCTAA\tIIIIIIIIIIIIIIIIIIIIIIIDII:\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:2:192:1456\t161\tchrM\t9071\t3\t27M\t=\t9255\t0\tACGAAACCACATAAATCAAGCCCTACT\tIII;IEIIDI7III+III*?I@CH+5I\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:63:192:470\t97\tchrM\t14787\t255\t27M\t=\t14982\t0\tGCAGATAAAATTCCATTTCACCCCTAC\tIIIIIIIIIIIIIIFIII=B5042:4E\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:49:528:63\t83\tchrM\t14963\t255\t27M\t=\t14829\t0\tTTTCCTATTTGCATACGCCATTCTACG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:98:856:1516\t145\tchrX\t20257960\t255\t27M\t=\t20256746\t0\tTACCCGGATTTAAGATGTACCCCATTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:28:1174:110\t145\tchrX\t53916348\t255\t27M\t=\t53916153\t0\tTGAATGTCAGCATCATTGACCCACAAA\tIIIIFIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:58:663:410\t147\tchrX\t75006902\t255\t27M\t=\t75006834\t0\tTCAGGTGGTTTACAGTGTTCTGACAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n\\ 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