Index: galaxy-central/test-data/unix_awk_input1.txt
===================================================================
--- galaxy-central/test-data/unix_awk_input1.txt (revision 3)
+++ galaxy-central/test-data/unix_awk_input1.txt (revision 3)
@@ -0,0 +1,10 @@
+chr10	0.4
+chr1	1.4
+chrM	3e-1
+chr2	1.1e2
+chr15	3.14e-2
+chr15	0.0314
+chr4	0.1
+chr20	0.9
+chr22	+1.3
+chrX	-0.3
Index: galaxy-central/test-data/replace_text_in_line_input1.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_line_input1.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_line_input1.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7  56632  56652   D17003_CTCF_R6  310  +
+chr7  56736  56756   D17003_CTCF_R7  354  +
+chr7  56761  56781   D17003_CTCF_R4  220  +
Index: galaxy-central/test-data/unix_grep_input1.txt
===================================================================
--- galaxy-central/test-data/unix_grep_input1.txt (revision 3)
+++ galaxy-central/test-data/unix_grep_input1.txt (revision 3)
@@ -0,0 +1,152 @@
+>FC0000042:5:1:220:1502
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:34:1398
+GATCTCAGTCCACCGCTGGGATTAACCTTGCCCCCC
+>FC0000042:5:1:164:1396
+TATCTTATAGATATTTCCCTCTATACTAGTGACCCC
+>FC0000042:5:1:333:925
+GAGCTTATAGCTTGTTATATACGTCAACCCCCCCCC
+>FC0000042:5:1:204:1476
+GTACTTATATAGATACAAAATATGTATAGGATTGTC
+>FC0000042:5:1:119:1511
+GATCTGCATGACCTGGGATTTGTTGGACCCCCCCCC
+>FC0000042:5:1:202:1487
+CATGTATAGTCTCCAGTCTATACAACAACCCCCCCC
+>FC0000042:5:1:182:1434
+GCTATAGAAATGTTAACATCGAATGTACATTATAAC
+>FC0000042:5:1:627:866
+AATATAGATATGGGACAAAACACATTTAGACCCCCC
+>FC0000042:5:1:24:1357
+GATATAATATCAATATCAATCCACGCTTGTTCCCCC
+>FC0000042:5:1:187:1492
+TATAGAAGCAGAAGAAACAACCTACTTTCACATGTT
+>FC0000042:5:1:45:1344
+CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC
+>FC0000042:5:1:87:1299
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:206:1341
+GATATATAGCAGTGACCACCTCTAAGCCCCCCCCCC
+>FC0000042:5:1:144:929
+GCCCTGGCATATTGTCAATATCTTTAAACCCCCCCC
+>FC0000042:5:1:662:820
+TGTCTTTTCGATTTTTTTCTTTGCGTCACCCCCCCC
+>FC0000042:5:1:53:1507
+GACCTCACTGTGGCATGAATCATACATTCCCCCCCC
+>FC0000042:5:1:182:1502
+AATGCTTGGCAAAGCTCAACTTCGTTGCCCCCCCCC
+>FC0000042:5:1:194:1423
+GATCCTATAGGTCTCGATTGGTCTTTTATTCTTTTT
+>FC0000042:5:1:35:1444
+GCTATAGCACGGCATAGTGCGATACTAGTACCCCCC
+>FC0000042:5:1:667:872
+GACTATAGGCGGAATGATAATGTCAAATAAGTAGTT
+>FC0000042:5:1:147:1438
+GATCAAGGAGACTAGGGAGGTAGGAGTTACTCCCCC
+>FC0000042:5:1:467:510
+GAACCACTATAGTGACATGGAACACGCGTGAACCCC
+>FC0000042:5:1:1553:1707
+TATAGTTACCCTACTGGGCCGACGATTCCCTTACGA
+>FC0000042:5:1:207:964
+AATCTATAGATTTTTCTATTATTGTGTCCTCACCCC
+>FC0000042:5:1:169:1468
+GCTCTATAGTTCGAGTTACCAAACTCTTCCCCCCCC
+>FC0000042:5:1:42:1465
+GCTCTTTAGGTTTGAACCTGTAGACTTGAGGGGCAT
+>FC0000042:5:1:55:1331
+GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT
+>FC0000042:5:1:175:1501
+GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC
+>FC0000042:5:1:221:1465
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+>FC0000042:5:1:196:1450
+AATATAGTCTATCCAACAAGATGTAACCCCCCCCCC
+>FC0000042:5:1:86:1413
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+>FC0000042:5:1:453:514
+GATATCTTCGTTTTATATTGAAACTGGCCCCCCCCC
+>FC0000042:5:1:150:1415
+TATAGGGCCCTGTATGGTTGCTTGACTAGGGGCTGC
+>FC0000042:5:1:191:1475
+GATCCATCCCAATCTCTACGATTGAAAGCATCGGGA
+>FC0000042:5:1:26:1407
+GTTATAGAGGCGGGAAGGTGAGAATGCCCCCCCCCC
+>FC0000042:5:1:107:1407
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:388:780
+GATCTATAGCTTCTTTAGCTTGGAAACTGGTCAGCC
+>FC0000042:5:1:223:1535
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:145:783
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:449:876
+GACCATCAATCAGGTGGAAAGCAGGGCCCCCCCCCC
+>FC0000042:5:1:212:1325
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+>FC0000042:5:1:194:1485
+GAACCGAATCCAACCTGTTTCATTCCTCAGATCCCC
+>FC0000042:5:1:507:494
+GATCTTATAGAATTTTTGACAACATAAGTTACCCCC
+>FC0000042:5:1:416:938
+AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC
+>FC0000042:5:1:633:480
+GAGCTGTGTGCATCTGTCCTGAGAGAGGCAAGATTT
+>FC0000042:5:1:53:1443
+GTAATGTTATAGCTAGGATTTTGGAGTTTGGTCCTC
+>FC0000042:5:1:45:915
+GTATAGCAGCCTAATAAGGAGCTGGGGACCCCCCCC
+>FC0000042:5:1:39:1343
+GTTCTATTTTCGATAAAACTGAACCACCCCCCCCCC
+>FC0000042:5:1:46:1501
+GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT
+>FC0000042:5:1:187:1507
+GAACTAATCCTGATTTATACAACGGCTCCCCCCCCC
+>FC0000042:5:1:91:1364
+AATTTATAGCCACTCTAATTCCGTTTGGTTCCCCCC
+>FC0000042:5:1:1542:1751
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>FC0000042:5:1:146:886
+GATCTACGATGTACCTTACGCCTCCGAGCATCCCCC
+>FC0000042:5:1:615:861
+GATCTACATTATAGATAATGAAGTTCCATTTCCCCC
+>FC0000042:5:1:52:792
+GATGTGGTATAGAGAGCAATTCGTTGGTTTTGCCCC
+>FC0000042:5:1:153:1433
+GGTCTTTCTATAGAACGGAACGATATATTTTTCCCC
+>FC0000042:5:1:540:800
+GAGCGAAAGTGATAGATGGAGGACTATATCTGCCCC
+>FC0000042:5:1:160:1344
+GGTGTACTATAGCTATTAAGTCCAATCATGATAATA
+>FC0000042:5:1:544:413
+GATCTCTGGAAAATATAAACCGGTGACCCCCCCCCC
+>FC0000042:5:1:579:895
+AGTCTCGAATCAATGTATTTCATCGTGGTAATCCCC
+>FC0000042:5:1:468:495
+TATTGATGCTCCCTGCCTGAAAGATACCCCCCCCCC
+>FC0000042:5:1:383:831
+CTTCATGAATCTACTGTTGGCGTTTATTTTATCTGG
+>FC0000042:5:1:112:1416
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+>FC0000042:5:1:37:1299
+GATCGTGAGCTCTGTACCGGAAGTTCGTGGCTGCCA
+>FC0000042:5:1:205:780
+TATAGTGTTCCACAAAGACTAGGTAACGCTTCATTT
+>FC0000042:5:1:33:702
+GAACGGACTATAGCCGGTATCCAAACATAAATGTTC
+>FC0000042:5:1:54:1019
+AATCGCAGCATTCTGACACACAGGTTTCGGATGTAC
+>FC0000042:5:1:587:867
+TATCTAATGTCATATTTTCAGACAAATTACTAGAAA
+>FC0000042:5:1:319:990
+GATTTGTAAATTACTTCGAACATAGAAGTTCCCCCC
+>FC0000042:5:1:453:829
+GAACTTACGGCATTAAGTTTAATCTTCAGCCACCCC
+>FC0000042:5:1:159:1470
+GATCTGATAGTGTTGCGACGTAAATAAGTCCCCCCC
+>FC0000042:5:1:487:820
+GATCTCGCAGGGATCAGTTATCCAGGTATTCCCCCC
+>FC0000042:5:1:48:371
+AATCTATAATCTTTACCCGAGTTTAAGTCCCCCCCC
+>FC0000042:5:1:1346:1739
+GATATAGGTTATACGTTTTTAGTCTTAGAGAAGTTT
+>FC0000042:5:1:661:459
+GATCTGCTTTAACGATTGAGGACGATGCCCCCCCCC
Index: galaxy-central/test-data/unix_cut_input1.txt
===================================================================
--- galaxy-central/test-data/unix_cut_input1.txt (revision 3)
+++ galaxy-central/test-data/unix_cut_input1.txt (revision 3)
@@ -0,0 +1,4 @@
+fruit	color	weight	price
+apple	red	1.4	0.4
+orange	orange	1.1	0.2
+banana	yellow	0.9	0.35
Index: galaxy-central/test-data/unix_cut_output1.txt
===================================================================
--- galaxy-central/test-data/unix_cut_output1.txt (revision 3)
+++ galaxy-central/test-data/unix_cut_output1.txt (revision 3)
@@ -0,0 +1,4 @@
+fruit	weight	price
+apple	1.4	0.4
+orange	1.1	0.2
+banana	0.9	0.35
Index: galaxy-central/test-data/unix_grep_output1.txt
===================================================================
--- galaxy-central/test-data/unix_grep_output1.txt (revision 3)
+++ galaxy-central/test-data/unix_grep_output1.txt (revision 3)
@@ -0,0 +1,14 @@
+>FC0000042:5:1:182:1434
+GCTATAGAAATGTTAACATCGAATGTACATTATAAC
+>FC0000042:5:1:45:1344
+CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC
+>FC0000042:5:1:55:1331
+GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT
+>FC0000042:5:1:175:1501
+GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC
+>FC0000042:5:1:416:938
+AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC
+>FC0000042:5:1:46:1501
+GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT
+>FC0000042:5:1:33:702
+GAACGGACTATAGCCGGTATCCAAACATAAATGTTC
Index: galaxy-central/test-data/unix_sort_input1.txt
===================================================================
--- galaxy-central/test-data/unix_sort_input1.txt (revision 3)
+++ galaxy-central/test-data/unix_sort_input1.txt (revision 3)
@@ -0,0 +1,10 @@
+chr10	0.4
+chr1	1.4
+chrM	3e-1
+chr2	1.1e2
+chr15	3.14e-2
+chr15	0.0314
+chr4	0.1
+chr20	0.9
+chr22	+1.3
+chrX	-0.3
Index: galaxy-central/test-data/unix_sort_output1.txt
===================================================================
--- galaxy-central/test-data/unix_sort_output1.txt (revision 3)
+++ galaxy-central/test-data/unix_sort_output1.txt (revision 3)
@@ -0,0 +1,10 @@
+chr2	1.1e2
+chr1	1.4
+chr22	+1.3
+chr20	0.9
+chr10	0.4
+chrM	3e-1
+chr4	0.1
+chr15	0.0314
+chr15	3.14e-2
+chrX	-0.3
Index: galaxy-central/test-data/replace_text_in_column_output1.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_column_output1.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_column_output1.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7  56632  56652   D17003_CTCF_R6  310  +
+chr7  56736  56756   D17003_CTCF_R7  354  +
+chr7  56761  56781   D17003_CTCF_R4  220  +
Index: galaxy-central/test-data/unix_sort_output2.txt
===================================================================
--- galaxy-central/test-data/unix_sort_output2.txt (revision 3)
+++ galaxy-central/test-data/unix_sort_output2.txt (revision 3)
@@ -0,0 +1,9 @@
+chrX	-0.3
+chr15	3.14e-2
+chr4	0.1
+chrM	3e-1
+chr10	0.4
+chr20	0.9
+chr22	+1.3
+chr1	1.4
+chr2	1.1e2
Index: galaxy-central/test-data/remove_ending_output1.txt
===================================================================
--- galaxy-central/test-data/remove_ending_output1.txt (revision 3)
+++ galaxy-central/test-data/remove_ending_output1.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7  56632  56652   D17003_CTCF_R6  310  +
+chr7  56736  56756   D17003_CTCF_R7  354  +
+chr7  56761  56781   D17003_CTCF_R4  220  +
Index: galaxy-central/test-data/replace_text_in_column_output2.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_column_output2.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_column_output2.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7	56632	56652	D17003_6R_FCTC	310	+
+chr7	56736	56756	D17003_7R_FCTC	354	+
+chr7	56761	56781	D17003_4R_FCTC	220	+
Index: galaxy-central/test-data/replace_text_in_line_output1.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_line_output1.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_line_output1.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7	56632	56652	D17003_FOOBAR_R6	310	+
+chr7	56736	56756	D17003_FOOBAR_R7	354	+
+chr7	56761	56781	D17003_FOOBAR_R4	220	+
Index: galaxy-central/test-data/unix_sort_output3.txt
===================================================================
--- galaxy-central/test-data/unix_sort_output3.txt (revision 3)
+++ galaxy-central/test-data/unix_sort_output3.txt (revision 3)
@@ -0,0 +1,10 @@
+chr1	1.4
+chr2	1.1e2
+chr4	0.1
+chr10	0.4
+chr15	0.0314
+chr15	3.14e-2
+chr20	0.9
+chr22	+1.3
+chrM	3e-1
+chrX	-0.3
Index: galaxy-central/test-data/replace_text_in_column_input1.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_column_input1.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_column_input1.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7  56632  56652   D17003_CTCF_R6  310  +
+chr7  56736  56756   D17003_CTCF_R7  354  +
+chr7  56761  56781   D17003_CTCF_R4  220  +
Index: galaxy-central/test-data/replace_text_in_line_output2.txt
===================================================================
--- galaxy-central/test-data/replace_text_in_line_output2.txt (revision 3)
+++ galaxy-central/test-data/replace_text_in_line_output2.txt (revision 3)
@@ -0,0 +1,3 @@
+chr7	56632	56652	D17003_6R_FCTC	310	+
+chr7	56736	56756	D17003_7R_FCTC	354	+
+chr7	56761	56781	D17003_4R_FCTC	220	+
Index: galaxy-central/test-data/unix_awk_output1.txt
===================================================================
--- galaxy-central/test-data/unix_awk_output1.txt (revision 3)
+++ galaxy-central/test-data/unix_awk_output1.txt (revision 3)
@@ -0,0 +1,4 @@
+12.6	chr1
+990	chr2
+8.1	chr20
+11.7	chr22
Index: galaxy-central/test-data/remove_ending_input1.txt
===================================================================
--- galaxy-central/test-data/remove_ending_input1.txt (revision 3)
+++ galaxy-central/test-data/remove_ending_input1.txt (revision 3)
@@ -0,0 +1,5 @@
+chr7  56632  56652   D17003_CTCF_R6  310  +
+chr7  56736  56756   D17003_CTCF_R7  354  +
+chr7  56761  56781   D17003_CTCF_R4  220  +
+chr7  56772  56792   D17003_CTCF_R7  372  +
+chr7  56775  56795   D17003_CTCF_R4  207  +
Index: galaxy-central/test-data/unix_grep_output2.html
===================================================================
--- galaxy-central/test-data/unix_grep_output2.html (revision 3)
+++ galaxy-central/test-data/unix_grep_output2.html (revision 3)
@@ -0,0 +1,9 @@
+<html><body><pre>
+GCTATAG<font color="blue"><b>AAATGT</b></font>TAACATCGAATGTACATTATAAC
+CAGCTAACAATC<font color="blue"><b>AAGCGT</b></font>TACAGATTAGCCCCCCCC
+GAACTTGCGTAACGTACAAAAATGCAAGCA<font color="blue"><b>AAAAGT</b></font>
+GCTCTGTTAATCTAGA<font color="blue"><b>AAATGT</b></font>GTCTCCCCCCCCCC
+<font color="blue"><b>AATCGT</b></font>ATAGCTCGGGCCGGATACTAGTACACCCCC
+GATATAGTGGATAACTAATGCTCCCCCAG<font color="blue"><b>AACTGT</b></font>T
+GAACGGACTATAGCCGGTATCCAAACAT<font color="blue"><b>AAATGT</b></font>TC
+</pre></body></html>