Repository 'macs2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/macs2

Changeset 14:c16dbe4e2db2 (2018-08-06)
Previous changeset 13:01cded2297b7 (2018-05-04) Next changeset 15:c33686854b19 (2018-10-15)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
modified:
macs2_callpeak.xml
test-data/callpeak_bampe_narrow.bed
test-data/callpeak_part.tabular
b
diff -r 01cded2297b7 -r c16dbe4e2db2 macs2_callpeak.xml
--- a/macs2_callpeak.xml Fri May 04 21:39:56 2018 -0400
+++ b/macs2_callpeak.xml Mon Aug 06 10:41:57 2018 -0400
[
b'@@ -1,4 +1,4 @@\n-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09">\n+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09">\n     <description>Call peaks from alignment results</description>\n     <macros>\n         <import>macs2_macros.xml</import>\n@@ -8,21 +8,25 @@\n     <expand macro="stdio" />\n     <expand macro="version_command" />\n     <command><![CDATA[\n+        #import re\n+\n         @home_dir@\n-\n         #set $temp_stderr = \'macs2_stderr\'\n+\n         (macs2 callpeak\n \n-            --name \'MACS2\'\n-\n             ## Treatment File(s)\n \n             #if str($treatment.t_multi_select) == "Yes":\n                 -t ${ \' \'.join( [ "\'%s\'" %  $x for $x in $treatment.input_treatment_file] ) }\n+                #set identifier = re.sub(\'[^\\w\\-]\', \'_\', str($treatment.input_treatment_file[0].element_identifier))\n             #else\n                 -t \'$treatment.input_treatment_file\'\n+                #set identifier = re.sub(\'[^\\w\\-]\', \'_\', str($treatment.input_treatment_file.element_identifier))\n             #end if\n \n+            --name $identifier\n+\n             ## Control File(s)\n \n             #if str($control.c_select) == "Yes":\n@@ -98,24 +102,24 @@\n         2>&1 > $temp_stderr)\n         #if "peaks_tabular" in str($outputs).split(\',\'):\n             &&\n-            cp MACS2_peaks.xls \'${ output_tabular }\'\n+            cp ${identifier}_peaks.xls \'${ output_tabular }\'\n         #end if\n \n         ## run R to create pdf from model script\n         #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(\',\') and $format != "BAMPE":\n             &&\n-            Rscript MACS2_model.r > MACS2_model.r.log\n+            Rscript ${identifier}_model.r > ${identifier}_model.r.log\n         #end if\n \n         #if \'html\' in str($outputs).split(\',\'):\n             ## if output files exists, move them to the files_path and create a html result page linking to them\n             &&\n             (\n-            count=`ls -1 MACS2* 2>/dev/null | wc -l`;\n+            count=`ls -1 ${identifier}* 2>/dev/null | wc -l`;\n             if [ \\$count != 0 ];\n             then\n                 mkdir \'${ output_extra_files.files_path }\' &&\n-                cp -r MACS2* \'${ output_extra_files.files_path }\' &&\n+                cp -r ${identifier}* \'${ output_extra_files.files_path }\' &&\n                 python \'$__tool_directory__/dir2html.py\'\n                     \'${ output_extra_files.files_path }\' $temp_stderr > \'${ output_extra_files }\';\n             fi;\n@@ -202,7 +206,7 @@\n         </conditional>\n \n         <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">\n-            <option value="peaks_tabular">Peaks as tabular file</option>\n+            <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>\n             <option value="summits">Peak summits</option>\n             <option value="bdg" >Scores in bedGraph files (--bdg)</option>\n             <option value="html">Summary page (html)</option>\n@@ -246,31 +250,31 @@\n         <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">\n             <filter> outputs and \'peaks_tabular\' in outputs</filter>\n         </data>\n-        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">\n+        <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">\n             <filter>\n             ((\n               advanced_options[\'broad_options\'][\'broad_options_selector\'] == "broad"\n             ))\n     '..b'C**.\n \n     Example:\n \n     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============\n     **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)**  **fold_enrichment** **-log10(qvalue)**  **name**\n     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============\n-    chr1    840082    840400  319        840240         4.00       10.50944            4.89872             6.91052             MACS2_peak_1\n-    chr1    919420    919785  366        919550         5.00       12.44148            5.85158             8.70936             MACS2_peak_2\n-    chr1    937221    937483  263        937375         4.00       10.06728            4.87632             6.61759             MACS2_peak_3\n+    chr1    840082    840400  319        840240         4.00       10.50944            4.89872             6.91052             treat1_peak_1\n+    chr1    919420    919785  366        919550         5.00       12.44148            5.85158             8.70936             treat1_peak_2\n+    chr1    937221    937483  263        937375         4.00       10.06728            4.87632             6.61759             treat1_peak_3\n     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============\n \n     Columns contain the following data:\n@@ -454,9 +458,9 @@\n     ======= ========= ======= ============ =======\n     1          2        3          4        **5**\n     ======= ========= ======= ============ =======\n-    chr1    840239    840240  MACS2_peak_1 6.91052\n-    chr1    919549    919550  MACS2_peak_2 8.70936\n-    chr1    937374    937375  MACS2_peak_3 6.61759\n+    chr1    840239    840240  treat1_peak_1 6.91052\n+    chr1    919549    919550  treat1_peak_2 8.70936\n+    chr1    937374    937375  treat1_peak_3 6.61759\n     ======= ========= ======= ============ =======\n \n     Columns contain the following data:\n@@ -513,9 +517,9 @@\n     ======= ========= ======= ============ ==== === ======= ======= =======\n     1        2         3       4            5    6   7       8       9\n     ======= ========= ======= ============ ==== === ======= ======= =======\n-    chr1    840081    840400  MACS2_peak_1  52   .  4.08790 8.57605 5.21506\n-    chr1    919419    919785  MACS2_peak_2  56   .  4.37270 8.90436 5.60462\n-    chr1    937220    937483  MACS2_peak_3  48   .  4.02343 8.06676 4.86861\n+    chr1    840081    840400  treat1_peak_1  52   .  4.08790 8.57605 5.21506\n+    chr1    919419    919785  treat1_peak_2  56   .  4.37270 8.90436 5.60462\n+    chr1    937220    937483  treat1_peak_3  48   .  4.02343 8.06676 4.86861\n     ======= ========= ======= ============ ==== === ======= ======= =======\n \n \n@@ -541,9 +545,9 @@\n     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n     1       2         3       4            5    6    7       8       9   10  11  12  13      14     15\n     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n-    chr1    840081    840400  MACS2_peak_1  52   .  840081  840400   0   1  319  0  4.08790 8.57605 5.21506\n-    chr1    919419    919785  MACS2_peak_2  56   .  919419  919785   0   1  366  0  4.37270 8.90436 5.60462\n-    chr1    937220    937483  MACS2_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861\n+    chr1    840081    840400  treat1_peak_1  52   .  840081  840400   0   1  319  0  4.08790 8.57605 5.21506\n+    chr1    919419    919785  treat1_peak_2  56   .  919419  919785   0   1  366  0  4.37270 8.90436 5.60462\n+    chr1    937220    937483  treat1_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861\n     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n \n Columns contain the following data:\n'
b
diff -r 01cded2297b7 -r c16dbe4e2db2 test-data/callpeak_bampe_narrow.bed
--- a/test-data/callpeak_bampe_narrow.bed Fri May 04 21:39:56 2018 -0400
+++ b/test-data/callpeak_bampe_narrow.bed Mon Aug 06 10:41:57 2018 -0400
b
@@ -1,1 +1,1 @@
-gi|251831106|ref|NC_012920.1| 0 251 MACS2_peak_1 3056 . 44.99989 308.04297 305.64328 56
+gi|251831106|ref|NC_012920.1| 0 251 bwa-mem-test1_bam_peak_1 3056 . 44.99989 308.04297 305.64328 56
b
diff -r 01cded2297b7 -r c16dbe4e2db2 test-data/callpeak_part.tabular
--- a/test-data/callpeak_part.tabular Fri May 04 21:39:56 2018 -0400
+++ b/test-data/callpeak_part.tabular Mon Aug 06 10:41:57 2018 -0400
[
b"@@ -1,100 +1,100 @@\n+# This file is generated by MACS version 2.1.1.20160309\n+# Command line: callpeak -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat --name ChIP_200K_bed -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat --format BED --gsize 3300000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300\n+# ARGUMENTS LIST:\n+# name = ChIP_200K_bed\n+# format = BED\n+# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat']\n+# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat']\n+# effective genome size = 3.30e+09\n+# band width = 300\n+# model fold = [5, 50]\n+# qvalue cutoff = 5.00e-02\n+# Larger dataset will be scaled towards smaller dataset.\n+# Range for calculating regional lambda is: 1000 bps and 10000 bps\n+# Broad region calling is off\n+# Paired-End mode is off\n \n+# tag size is determined as 100 bps\n+# total tags in treatment: 199977\n+# tags after filtering in treatment: 199583\n+# maximum duplicate tags at the same position in treatment = 1\n+# Redundant rate in treatment: 0.00\n+# total tags in control: 199978\n+# tags after filtering in control: 199867\n+# maximum duplicate tags at the same position in control = 1\n+# Redundant rate in control: 0.00\n+# d = 254\n+# alternative fragment length(s) may be 254 bps\n chr\tstart\tend\tlength\tabs_summit\tpileup\t-log10(pvalue)\tfold_enrichment\t-log10(qvalue)\tname\n-chr1\t840082\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_1\n-chr1\t919420\t919785\t366\t919550\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_2\n-chr1\t937221\t937483\t263\t937375\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_3\n-chr1\t954743\t954996\t254\t954814\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_4\n-chr1\t994763\t995016\t254\t994906\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_5\n-chr1\t1057395\t1057648\t254\t1057509\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_6\n-chr1\t1240580\t1241004\t425\t1240777\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_7\n-chr1\t1307393\t1307735\t343\t1307601\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_8\n-chr1\t1440351\t1440633\t283\t1440462\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_9\n-chr1\t1555433\t1555725\t293\t1555571\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_10\n-chr1\t1590668\t1590946\t279\t1590840\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_11\n-chr1\t1837669\t1838104\t436\t1837886\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_12\n-chr1\t1840366\t1840828\t463\t1840547\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_13\n-chr1\t1976400\t1976653\t254\t1976469\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_14\n-chr1\t2071302\t2071627\t326\t2071423\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_15\n-chr1\t2105717\t2106140\t424\t2105919\t4.00\t7.70001\t4.64644\t4.60940\tMACS2_peak_16\n-chr1\t2126522\t2126861\t340\t2126648\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_17\n-chr1\t2246521\t2246954\t434\t2246712\t5.00\t9.59761\t5.57573\t6.23289\tMACS2_peak_18\n-chr1\t2313158\t2313560\t403\t2313353\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_19\n-chr1\t2345828\t2346242\t415\t2346028\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_20\n-chr1\t2510055\t2510308\t254\t2510213\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_21\n-chr1\t3341408\t3341661\t254\t3341461\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_22\n-chr1\t3369639\t3369892\t254\t3369863\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_23\n-chr1\t3400441\t3400769\t329\t3400610\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_24\n-chr1\t3407841\t3408094\t254\t3407975\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_25\n-chr1\t3481748\t3482245\t498\t3481863\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_26\n-chr1\t3535562\t3535821\t260\t3535663\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_27\n-chr1\t3537757\t3538010\t254\t3537960\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_28\n-chr1\t3593610\t3593863\t254\t3593838\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_29\n-chr1\t3640884\t3641366\t483\t3641134\t12.00\t30.54970\t12.67843\t24.90331\tMACS2_peak_30\n-chr1\t3702144\t3702397\t254\t3702260\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_31\n-chr1\t3773699\t3774058\t360\t3773876\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_32\n-chr1\t3827306\t3827722\t"..b'0\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_26\n+chr1\t3535562\t3535821\t260\t3535663\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_27\n+chr1\t3537757\t3538010\t254\t3537960\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_28\n+chr1\t3593610\t3593863\t254\t3593838\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_29\n+chr1\t3640884\t3641366\t483\t3641134\t12.00\t30.54970\t12.67843\t24.90331\tChIP_200K_bed_peak_30\n+chr1\t3702144\t3702397\t254\t3702260\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_31\n+chr1\t3773699\t3774058\t360\t3773876\t7.00\t19.11990\t7.87896\t14.58582\tChIP_200K_bed_peak_32\n+chr1\t3827306\t3827722\t417\t3827525\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_33\n+chr1\t4712784\t4713037\t254\t4712904\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_34\n+chr1\t4886187\t4886440\t254\t4886326\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_35\n+chr1\t5569919\t5570198\t280\t5570056\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_36\n+chr1\t5574777\t5575080\t304\t5574838\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_37\n+chr1\t5805838\t5806091\t254\t5805965\t2.00\t6.22382\t2.95461\t3.18932\tChIP_200K_bed_peak_38\n+chr1\t5976146\t5976399\t254\t5976235\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_39\n+chr1\t6094646\t6094899\t254\t6094678\t2.00\t6.22382\t2.95461\t3.18932\tChIP_200K_bed_peak_40\n+chr1\t6112957\t6113210\t254\t6113135\t3.00\t6.57684\t3.80689\t3.50364\tChIP_200K_bed_peak_41\n+chr1\t6265253\t6265640\t388\t6265437\t6.00\t11.56197\t6.50502\t7.91704\tChIP_200K_bed_peak_42\n+chr1\t6305229\t6305482\t254\t6305299\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_43\n+chr1\t6306874\t6307127\t254\t6307013\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_44\n+chr1\t6403481\t6403843\t363\t6403679\t6.00\t16.40316\t6.89409\t12.16639\tChIP_200K_bed_peak_45\n+chr1\t6464657\t6465096\t440\t6464869\t6.00\t11.56197\t6.50502\t7.91704\tChIP_200K_bed_peak_46\n+chr1\t6483604\t6483857\t254\t6483739\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_47\n+chr1\t6498110\t6498494\t385\t6498258\t6.00\t14.88256\t6.82684\t10.84922\tChIP_200K_bed_peak_48\n+chr1\t6535513\t6535838\t326\t6535591\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_49\n+chr1\t6614468\t6614882\t415\t6614708\t4.00\t10.06728\t4.87632\t6.61759\tChIP_200K_bed_peak_50\n+chr1\t6706586\t6706931\t346\t6706743\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_51\n+chr1\t6761833\t6762203\t371\t6762039\t7.00\t14.98313\t7.61377\t10.92185\tChIP_200K_bed_peak_52\n+chr1\t6780092\t6780471\t380\t6780329\t6.00\t16.40316\t6.89409\t12.16639\tChIP_200K_bed_peak_53\n+chr1\t6787475\t6787900\t426\t6787704\t7.00\t19.11990\t7.87896\t14.58582\tChIP_200K_bed_peak_54\n+chr1\t6949953\t6950377\t425\t6950153\t5.00\t10.64473\t5.71033\t7.17293\tChIP_200K_bed_peak_55\n+chr1\t7102753\t7103077\t325\t7102915\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_56\n+chr1\t7278317\t7278718\t402\t7278483\t6.00\t16.40316\t6.89409\t12.16639\tChIP_200K_bed_peak_57\n+chr1\t7868456\t7868722\t267\t7868577\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_58\n+chr1\t7962797\t7963068\t272\t7962862\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_59\n+chr1\t8042368\t8042722\t355\t8042491\t6.00\t14.88256\t6.82684\t10.84922\tChIP_200K_bed_peak_60\n+chr1\t8075039\t8075466\t428\t8075252\t6.00\t12.78498\t6.66205\t9.02328\tChIP_200K_bed_peak_61\n+chr1\t8076577\t8076851\t275\t8076739\t4.00\t8.57130\t4.75861\t5.28944\tChIP_200K_bed_peak_62\n+chr1\t8091217\t8091506\t290\t8091352\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_63\n+chr1\t8374359\t8374715\t357\t8374570\t6.00\t16.40316\t6.89409\t12.16639\tChIP_200K_bed_peak_64\n+chr1\t8408996\t8409352\t357\t8409218\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_65\n+chr1\t8731417\t8731750\t334\t8731570\t4.00\t10.06728\t4.87632\t6.61759\tChIP_200K_bed_peak_66\n+chr1\t8786590\t8786948\t359\t8786756\t7.00\t12.59445\t7.26312\t8.86075\tChIP_200K_bed_peak_67\n+chr1\t8908916\t8909169\t254\t8909002\t2.00\t5.57376\t2.92579\t2.70690\tChIP_200K_bed_peak_68\n+chr1\t8978204\t8978524\t321\t8978356\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_69\n+chr1\t9048092\t9048380\t289\t9048260\t4.00\t8.57130\t4.75861\t5.28944\tChIP_200K_bed_peak_70\n+chr1\t9065105\t9065592\t488\t9065349\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_71\n+chr1\t9069997\t9070429\t433\t9070211\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_72\n'