--- a/sampline.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-<tool id="sampline" name="sample">
-  <description>records from a file</description>
-  <command interpreter="python">sampline.py --input=$input --output=$out_file1 --nSample=$nSample --recSize=$recSize --nSkip=$nSkip $replacement</command>
-  <inputs>
-    <param name="input" format="txt" type="data" label="Original file"/>
-    <param name="nSample" size="10" type="integer" value="100" label="Number of records to sample"/>
-    <param name="recSize" size="10" type="integer" value="1" label="Number of lines per record"/>
-    <param name="nSkip" size="10" type="integer" value="0" label="Number of top lines to output directly (without sampling)"/>
-    <param name="replacement" label="Sampling with replacement" type="boolean" truevalue="--replacement" falsevalue="" checked="False"/>
-  </inputs>
-  <outputs>
-    <data format="input" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <output name="out_file1" file="testmap.sampled"/>
-      <param name="input" value="test.map" ftype="TXT"/>
-      <param name="nSample" value="100"/>
-      <param name="recSize"  value="1" />
-      <param name="nSkip" value="0" />
-      <param name="replacement" value=""/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-This tool selects random records from a file. Each record is defined by a fixed number of lines.  
-
-- When doing over-sampling,  --replacement  option is enforced by default.
-
------
-
-**Example 1: sampling from a BED file**
-
-parameters::
-
-    1 line per record, sampling 5 lines, without replacement, output line 1 (track name) directly
-
-Input::
-
-    track name=test.bed
-    chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
-    chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
-    chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
-    chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
-    chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
-    chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
-    chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
-    chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
-    chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
-    chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
-
-Output::
-
-    track name=test.bed
-    chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
-    chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
-    chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
-    chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
-    chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	
-
-**Example 2: sampling reads from a fastq file**
-
-parameters::
-
-    4 line per record, sampling 3 records, without replacement
-
-Input::
-
-    @SRR066787.2496 WICMT-SOLEXA:8:1:28:2047 length=36
-    NNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-    +SRR066787.2496 WICMT-SOLEXA:8:1:28:2047 length=36
-    !!%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-    @SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
-    GTGATTAAGAAGAGACTGGCATCACTAAGGTGACAT
-    +SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
-    @A=BBCBBAA@:@:@@@:,?AB:B?BB=*2:@=?AA
-    @SRR066787.2498 WICMT-SOLEXA:8:1:28:704 length=36
-    GAACCCAATTTTCAAAGAAGTGTGACTGCTTGTTTC
-    +SRR066787.2498 WICMT-SOLEXA:8:1:28:704 length=36
-    =?BAABBACCCCAA9>>A=>A?A;;@A>ABBABBB:
-    @SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
-    CGACTTCAGGCTCTCGCTAGCCTTCGCTTGACTGAC
-    +SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
-    BCCBCCB?A1ACAC>;@CCAAABB?8=BA>@?B?@:
-    @SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
-    TCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTC
-    +SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
-    ?.?.=9C8CCC:BACBCBC?CCC@CBBBCBBACAC8
-
-Output::
-
-    @SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
-    GTGATTAAGAAGAGACTGGCATCACTAAGGTGACAT
-    +SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
-    @A=BBCBBAA@:@:@@@:,?AB:B?BB=*2:@=?AA
-    @SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
-    CGACTTCAGGCTCTCGCTAGCCTTCGCTTGACTGAC
-    +SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
-    BCCBCCB?A1ACAC>;@CCAAABB?8=BA>@?B?@:
-    @SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
-    TCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTC
-    +SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
-    ?.?.=9C8CCC:BACBCBC?CCC@CBBBCBBACAC8
-
-  </help>
-</tool>