# HG changeset patch
# User jowong
# Date 1538082318 14400
# Node ID 231b21337c432d2cde9d4cbf6c473b7cfb70f3c2

planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3

diff -r 000000000000 -r 231b21337c43 add_sample_name_as_first_line.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_sample_name_as_first_line.py	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,23 @@
+import sys
+import argparse
+import re
+
+def Parser():
+  the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file")
+  the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file")
+  the_parser.add_argument('--output', required=True,  action="store", type=str, help="output file")
+  the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file")
+  args = the_parser.parse_args()
+  return args
+
+args=Parser()
+
+sample_name = re.sub('[_12]*.fastq.gz', '', args.sample.rstrip().lstrip())
+
+with open(args.input) as input:
+	with open(args.output, 'w') as output:
+		output.write(sample_name+"\n")
+		for line in input:
+			output.write(line)
+
+
diff -r 000000000000 -r 231b21337c43 add_sample_name_as_first_line.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_sample_name_as_first_line.xml	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,33 @@
+<tool id="my_addName" name="Add sample name as first line" version="0.1.0">
+  <description>to an existing tabular file</description>
+  <command interpreter="python">add_sample_name_as_first_line.py 
+    --input "$input" 
+    --sample "$input2.element_identifier" 
+    --output "$output"
+  </command>
+  <inputs>
+  <param format="tabular" name="input" type="data" label="to Dataset"  />
+  <param name="input2" format="data" type="data" label="sample"  />
+  </inputs>
+  <outputs>
+    <data name="output" format="tabular" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test.tab" ftype="tabular" />
+      <param name="input2" value="ABC_1.fastq.gz" />
+      <output name="output" file="test_with_header.tab" ftype="tabular"/>
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+Adds a new line with the name of the sample file and removing [_12].fastq.gz from the name if there is match to the pattern.
+Written by Johnathan Kwan Long Wong, johnathanwong4@gmail.com
+  </help>
+  <citations>
+    <citation type="bibtex">@UNPUBLISHED{Johnathan2018,
+      author = "Johnathan W"}</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r 231b21337c43 test-data/ABC_1.fastq.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ABC_1.fastq.gz	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,2114 @@
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+NC_000962.3	4232327	snp	A	G
+NC_000962.3	4236844	snp	G	A
+NC_000962.3	4237383	snp	C	A
+NC_000962.3	4240671	snp	C	T
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+NC_000962.3	4242643	snp	C	T
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+NC_000962.3	4247578	snp	G	A
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diff -r 000000000000 -r 231b21337c43 test-data/test.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tab	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,2114 @@
+CHROM	POS	TYPE	REF	ALT
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+NC_000962.3	4055964	snp	A	C
+NC_000962.3	4056416	snp	C	A
+NC_000962.3	4059904	snp	A	G
+NC_000962.3	4060824	snp	C	T
+NC_000962.3	4061113	snp	G	T
+NC_000962.3	4067152	snp	G	A
+NC_000962.3	4069292	snp	G	A
+NC_000962.3	4069797	snp	C	T
+NC_000962.3	4077177	snp	G	A
+NC_000962.3	4078863	snp	C	T
+NC_000962.3	4081987	snp	G	C
+NC_000962.3	4081996	snp	G	C
+NC_000962.3	4083360	snp	T	G
+NC_000962.3	4085200	snp	G	C
+NC_000962.3	4089058	snp	T	C
+NC_000962.3	4093719	snp	G	A
+NC_000962.3	4095295	snp	T	C
+NC_000962.3	4096190	snp	G	A
+NC_000962.3	4100975	snp	T	C
+NC_000962.3	4101018	snp	C	T
+NC_000962.3	4105757	snp	C	T
+NC_000962.3	4106154	snp	C	T
+NC_000962.3	4107074	snp	T	C
+NC_000962.3	4107264	snp	C	T
+NC_000962.3	4111303	snp	G	C
+NC_000962.3	4112429	snp	T	C
+NC_000962.3	4113833	snp	C	T
+NC_000962.3	4115001	snp	G	C
+NC_000962.3	4115029	snp	G	A
+NC_000962.3	4116682	snp	T	C
+NC_000962.3	4116758	snp	C	T
+NC_000962.3	4117161	snp	C	A
+NC_000962.3	4118620	snp	G	T
+NC_000962.3	4119246	snp	T	C
+NC_000962.3	4120983	snp	A	G
+NC_000962.3	4123325	snp	C	T
+NC_000962.3	4125460	snp	C	T
+NC_000962.3	4126087	snp	T	G
+NC_000962.3	4126530	snp	G	A
+NC_000962.3	4130711	snp	G	C
+NC_000962.3	4133907	snp	G	A
+NC_000962.3	4137190	snp	T	C
+NC_000962.3	4138377	snp	A	G
+NC_000962.3	4142689	snp	G	A
+NC_000962.3	4145737	snp	A	G
+NC_000962.3	4148861	snp	G	A
+NC_000962.3	4150036	snp	G	T
+NC_000962.3	4151855	snp	A	G
+NC_000962.3	4155266	snp	C	G
+NC_000962.3	4155903	snp	G	T
+NC_000962.3	4156099	snp	C	A
+NC_000962.3	4156239	snp	A	G
+NC_000962.3	4156503	snp	C	T
+NC_000962.3	4158361	snp	A	G
+NC_000962.3	4159195	snp	T	C
+NC_000962.3	4161725	snp	G	T
+NC_000962.3	4162339	snp	A	G
+NC_000962.3	4163558	snp	G	C
+NC_000962.3	4163954	snp	T	C
+NC_000962.3	4169719	snp	C	T
+NC_000962.3	4171454	snp	G	A
+NC_000962.3	4179089	snp	C	T
+NC_000962.3	4182695	snp	G	A
+NC_000962.3	4187063	snp	G	A
+NC_000962.3	4187485	snp	T	C
+NC_000962.3	4187523	snp	A	G
+NC_000962.3	4187817	snp	A	G
+NC_000962.3	4189721	snp	G	T
+NC_000962.3	4190285	snp	T	C
+NC_000962.3	4190532	snp	A	C
+NC_000962.3	4190596	snp	A	C
+NC_000962.3	4195938	snp	G	A
+NC_000962.3	4197189	snp	A	G
+NC_000962.3	4200220	snp	A	G
+NC_000962.3	4201105	snp	G	A
+NC_000962.3	4202383	snp	A	C
+NC_000962.3	4204441	snp	A	G
+NC_000962.3	4205120	snp	A	G
+NC_000962.3	4210274	snp	A	G
+NC_000962.3	4210876	snp	T	C
+NC_000962.3	4215484	snp	G	C
+NC_000962.3	4216255	snp	C	G
+NC_000962.3	4217557	snp	A	G
+NC_000962.3	4221490	snp	C	G
+NC_000962.3	4222073	snp	A	G
+NC_000962.3	4222882	snp	A	G
+NC_000962.3	4223172	snp	T	C
+NC_000962.3	4231150	snp	G	A
+NC_000962.3	4231530	snp	C	A
+NC_000962.3	4232327	snp	A	G
+NC_000962.3	4236844	snp	G	A
+NC_000962.3	4237383	snp	C	A
+NC_000962.3	4240671	snp	C	T
+NC_000962.3	4241042	snp	A	G
+NC_000962.3	4242643	snp	C	T
+NC_000962.3	4243580	snp	G	A
+NC_000962.3	4244420	snp	G	C
+NC_000962.3	4245969	snp	C	T
+NC_000962.3	4247578	snp	G	A
+NC_000962.3	4247646	snp	A	C
+NC_000962.3	4250022	snp	T	G
+NC_000962.3	4250966	snp	G	A
+NC_000962.3	4251297	snp	G	C
+NC_000962.3	4255922	snp	A	G
+NC_000962.3	4257220	snp	A	G
+NC_000962.3	4261499	snp	G	A
+NC_000962.3	4263279	snp	A	G
+NC_000962.3	4264560	snp	G	A
+NC_000962.3	4269387	snp	T	G
+NC_000962.3	4269606	snp	A	G
+NC_000962.3	4275935	snp	A	G
+NC_000962.3	4276306	snp	C	T
+NC_000962.3	4277032	snp	G	C
+NC_000962.3	4280441	snp	C	A
+NC_000962.3	4281143	snp	C	G
+NC_000962.3	4281272	snp	G	A
+NC_000962.3	4287164	snp	A	G
+NC_000962.3	4287361	snp	C	T
+NC_000962.3	4289953	snp	A	G
+NC_000962.3	4290564	snp	G	T
+NC_000962.3	4290827	snp	C	G
+NC_000962.3	4293107	snp	G	A
+NC_000962.3	4296015	snp	G	A
+NC_000962.3	4296381	snp	G	T
+NC_000962.3	4301972	snp	C	T
+NC_000962.3	4302036	snp	T	C
+NC_000962.3	4303407	snp	A	C
+NC_000962.3	4306155	snp	C	T
+NC_000962.3	4306339	snp	G	T
+NC_000962.3	4307021	snp	C	T
+NC_000962.3	4307179	snp	G	A
+NC_000962.3	4307344	snp	C	G
+NC_000962.3	4313128	snp	C	T
+NC_000962.3	4314645	snp	A	G
+NC_000962.3	4314843	snp	G	A
+NC_000962.3	4316566	snp	C	G
+NC_000962.3	4323006	snp	G	A
+NC_000962.3	4326655	snp	G	A
+NC_000962.3	4329782	snp	G	A
+NC_000962.3	4334425	snp	G	C
+NC_000962.3	4336597	snp	C	A
+NC_000962.3	4336774	snp	C	T
+NC_000962.3	4337574	snp	A	G
+NC_000962.3	4338361	snp	C	T
+NC_000962.3	4338603	snp	G	A
+NC_000962.3	4338732	snp	G	A
+NC_000962.3	4344058	snp	T	C
+NC_000962.3	4345682	snp	C	T
+NC_000962.3	4348418	snp	G	A
+NC_000962.3	4349778	snp	G	A
+NC_000962.3	4351039	snp	G	T
+NC_000962.3	4351759	snp	G	C
+NC_000962.3	4354013	snp	G	A
+NC_000962.3	4355919	snp	G	T
+NC_000962.3	4356110	snp	G	C
+NC_000962.3	4357597	snp	C	G
+NC_000962.3	4357773	snp	G	A
+NC_000962.3	4357946	snp	C	T
+NC_000962.3	4361141	snp	G	A
+NC_000962.3	4363243	snp	A	C
+NC_000962.3	4366195	snp	T	C
+NC_000962.3	4366272	snp	G	C
+NC_000962.3	4367090	snp	G	A
+NC_000962.3	4367649	snp	A	G
+NC_000962.3	4369499	snp	G	A
+NC_000962.3	4372353	snp	G	C
+NC_000962.3	4374228	snp	T	C
+NC_000962.3	4375318	snp	G	A
+NC_000962.3	4375628	snp	G	T
+NC_000962.3	4377033	snp	G	C
+NC_000962.3	4379680	snp	C	G
+NC_000962.3	4382054	snp	T	C
+NC_000962.3	4382275	snp	G	T
+NC_000962.3	4383442	snp	T	C
+NC_000962.3	4383655	snp	A	G
+NC_000962.3	4384007	snp	C	G
+NC_000962.3	4385187	snp	A	G
+NC_000962.3	4386228	snp	T	C
+NC_000962.3	4390380	snp	A	G
+NC_000962.3	4393178	snp	A	G
+NC_000962.3	4394210	snp	G	C
+NC_000962.3	4395387	snp	A	G
+NC_000962.3	4398732	snp	G	A
+NC_000962.3	4399137	snp	G	A
+NC_000962.3	4401400	snp	A	G
+NC_000962.3	4407588	snp	T	C
+NC_000962.3	4407873	snp	C	A
+NC_000962.3	4408920	snp	A	G
+NC_000962.3	4408923	snp	C	T
+NC_000962.3	4410386	snp	G	T
+NC_000962.3	4411016	snp	G	A
diff -r 000000000000 -r 231b21337c43 test-data/test_with_header.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_with_header.tab	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,2115 @@
+ABC
+CHROM	POS	TYPE	REF	ALT
+NC_000962.3	1302	snp	C	A
+NC_000962.3	1977	snp	A	G
+NC_000962.3	2532	snp	T	C
+NC_000962.3	4013	snp	T	C
+NC_000962.3	6112	snp	G	C
+NC_000962.3	7362	snp	G	C
+NC_000962.3	7585	snp	G	C
+NC_000962.3	8452	snp	C	T
+NC_000962.3	9143	snp	T	C
+NC_000962.3	9260	snp	G	C
+NC_000962.3	9304	snp	G	A
+NC_000962.3	11879	snp	A	G
+NC_000962.3	13175	snp	A	G
+NC_000962.3	13298	snp	G	C
+NC_000962.3	13460	snp	A	G
+NC_000962.3	14401	snp	A	G
+NC_000962.3	14785	snp	T	C
+NC_000962.3	15088	snp	C	T
+NC_000962.3	15117	snp	C	G
+NC_000962.3	16526	snp	C	T
+NC_000962.3	21795	snp	G	A
+NC_000962.3	21819	snp	A	C
+NC_000962.3	22961	snp	T	G
+NC_000962.3	23174	snp	C	A
+NC_000962.3	26347	snp	C	G
+NC_000962.3	26959	snp	C	G
+NC_000962.3	27199	snp	G	A
+NC_000962.3	27469	snp	A	G
+NC_000962.3	27473	snp	G	T
+NC_000962.3	27996	snp	T	C
+NC_000962.3	31142	snp	C	T
+NC_000962.3	34044	snp	T	C
+NC_000962.3	36538	snp	T	C
+NC_000962.3	37031	snp	C	G
+NC_000962.3	39623	snp	C	G
+NC_000962.3	39758	snp	A	G
+NC_000962.3	41151	snp	C	A
+NC_000962.3	42281	snp	C	A
+NC_000962.3	42967	snp	G	C
+NC_000962.3	43945	snp	A	G
+NC_000962.3	46735	snp	G	A
+NC_000962.3	49976	snp	C	T
+NC_000962.3	51781	snp	C	G
+NC_000962.3	51949	snp	A	G
+NC_000962.3	54394	snp	A	G
+NC_000962.3	62049	snp	A	G
+NC_000962.3	63752	snp	C	T
+NC_000962.3	64028	snp	C	T
+NC_000962.3	65159	snp	G	A
+NC_000962.3	65663	snp	C	G
+NC_000962.3	66892	snp	C	G
+NC_000962.3	66937	snp	C	T
+NC_000962.3	68174	snp	T	C
+NC_000962.3	69989	snp	G	A
+NC_000962.3	70267	snp	G	T
+NC_000962.3	70816	snp	A	G
+NC_000962.3	71336	snp	G	C
+NC_000962.3	74737	snp	T	G
+NC_000962.3	75233	snp	C	A
+NC_000962.3	75940	snp	G	C
+NC_000962.3	79479	snp	T	C
+NC_000962.3	80616	snp	C	G
+NC_000962.3	83343	snp	C	T
+NC_000962.3	89200	snp	G	T
+NC_000962.3	89871	snp	C	T
+NC_000962.3	92199	snp	T	G
+NC_000962.3	97696	snp	T	C
+NC_000962.3	98966	snp	G	C
+NC_000962.3	103600	snp	A	G
+NC_000962.3	104712	snp	C	T
+NC_000962.3	104824	snp	C	A
+NC_000962.3	105045	snp	G	C
+NC_000962.3	106126	snp	T	C
+NC_000962.3	115499	snp	T	G
+NC_000962.3	116000	snp	T	G
+NC_000962.3	122109	snp	A	G
+NC_000962.3	123520	snp	T	C
+NC_000962.3	126803	snp	A	G
+NC_000962.3	126853	snp	G	A
+NC_000962.3	132417	snp	C	G
+NC_000962.3	132646	snp	G	T
+NC_000962.3	133839	snp	C	T
+NC_000962.3	137233	snp	C	T
+NC_000962.3	137673	snp	G	A
+NC_000962.3	139756	snp	T	C
+NC_000962.3	139954	snp	A	C
+NC_000962.3	143207	snp	T	C
+NC_000962.3	144433	snp	C	G
+NC_000962.3	144434	snp	C	T
+NC_000962.3	144564	snp	C	T
+NC_000962.3	146087	snp	T	C
+NC_000962.3	146788	snp	G	A
+NC_000962.3	146872	snp	C	T
+NC_000962.3	147970	snp	C	T
+NC_000962.3	149983	snp	G	C
+NC_000962.3	150052	snp	G	A
+NC_000962.3	150602	snp	C	A
+NC_000962.3	150609	snp	C	T
+NC_000962.3	150611	snp	C	T
+NC_000962.3	154191	snp	A	G
+NC_000962.3	154283	snp	T	C
+NC_000962.3	157364	snp	C	T
+NC_000962.3	160976	snp	C	G
+NC_000962.3	162226	snp	G	A
+NC_000962.3	167986	snp	C	T
+NC_000962.3	168787	snp	C	T
+NC_000962.3	177175	snp	G	C
+NC_000962.3	177857	snp	G	A
+NC_000962.3	188800	snp	T	C
+NC_000962.3	189948	snp	C	G
+NC_000962.3	194040	snp	C	A
+NC_000962.3	194681	snp	G	C
+NC_000962.3	195360	snp	T	C
+NC_000962.3	196642	snp	C	T
+NC_000962.3	196874	snp	C	T
+NC_000962.3	199470	snp	T	G
+NC_000962.3	200379	snp	C	T
+NC_000962.3	206339	snp	T	C
+NC_000962.3	206481	snp	C	G
+NC_000962.3	206484	snp	G	T
+NC_000962.3	211993	snp	C	A
+NC_000962.3	215238	snp	C	T
+NC_000962.3	217201	snp	T	C
+NC_000962.3	223942	snp	T	C
+NC_000962.3	225315	snp	G	A
+NC_000962.3	225323	snp	T	C
+NC_000962.3	225668	snp	C	T
+NC_000962.3	226676	snp	G	A
+NC_000962.3	227098	snp	T	C
+NC_000962.3	231114	snp	C	G
+NC_000962.3	233358	snp	A	C
+NC_000962.3	233364	snp	G	C
+NC_000962.3	234477	snp	T	G
+NC_000962.3	235681	snp	G	A
+NC_000962.3	236512	snp	C	T
+NC_000962.3	241465	snp	G	A
+NC_000962.3	243598	snp	A	G
+NC_000962.3	244550	snp	A	G
+NC_000962.3	251575	snp	G	A
+NC_000962.3	251669	snp	T	C
+NC_000962.3	254903	snp	C	A
+NC_000962.3	260282	snp	G	T
+NC_000962.3	261869	snp	T	C
+NC_000962.3	263057	snp	T	G
+NC_000962.3	263149	snp	A	C
+NC_000962.3	264298	snp	C	A
+NC_000962.3	264984	snp	C	G
+NC_000962.3	265554	snp	A	C
+NC_000962.3	272678	snp	C	T
+NC_000962.3	273568	snp	G	T
+NC_000962.3	278681	snp	C	G
+NC_000962.3	281454	snp	C	A
+NC_000962.3	282604	snp	A	T
+NC_000962.3	283614	snp	T	C
+NC_000962.3	285772	snp	A	C
+NC_000962.3	285871	snp	A	G
+NC_000962.3	290374	snp	T	C
+NC_000962.3	291977	snp	G	A
+NC_000962.3	294170	snp	G	A
+NC_000962.3	297236	snp	C	T
+NC_000962.3	297396	snp	G	A
+NC_000962.3	303414	snp	C	T
+NC_000962.3	304923	snp	A	G
+NC_000962.3	308312	snp	G	A
+NC_000962.3	309765	snp	C	T
+NC_000962.3	310973	snp	G	A
+NC_000962.3	311613	snp	G	T
+NC_000962.3	320180	snp	A	G
+NC_000962.3	325505	snp	T	C
+NC_000962.3	326002	snp	A	G
+NC_000962.3	331588	snp	G	A
+NC_000962.3	333212	snp	G	C
+NC_000962.3	333292	snp	A	G
+NC_000962.3	333892	snp	G	C
+NC_000962.3	337820	snp	G	A
+NC_000962.3	337959	snp	A	C
+NC_000962.3	338020	snp	A	C
+NC_000962.3	338100	snp	T	C
+NC_000962.3	339508	snp	C	T
+NC_000962.3	340372	snp	T	C
+NC_000962.3	342146	snp	A	C
+NC_000962.3	343281	snp	G	C
+NC_000962.3	344288	snp	C	G
+NC_000962.3	346275	snp	C	G
+NC_000962.3	350489	snp	G	C
+NC_000962.3	351875	snp	G	A
+NC_000962.3	356528	snp	A	G
+NC_000962.3	357582	snp	G	A
+NC_000962.3	361825	snp	T	C
+NC_000962.3	362007	snp	G	A
+NC_000962.3	367471	snp	G	A
+NC_000962.3	368353	snp	C	T
+NC_000962.3	368948	snp	T	C
+NC_000962.3	370575	snp	C	T
+NC_000962.3	372149	snp	G	A
+NC_000962.3	372913	snp	A	C
+NC_000962.3	375095	snp	C	G
+NC_000962.3	376774	snp	T	C
+NC_000962.3	378357	snp	T	G
+NC_000962.3	378939	snp	G	C
+NC_000962.3	381030	snp	A	G
+NC_000962.3	382822	snp	G	A
+NC_000962.3	384380	snp	A	C
+NC_000962.3	386432	snp	C	G
+NC_000962.3	390828	snp	T	C
+NC_000962.3	391030	snp	C	A
+NC_000962.3	391853	snp	A	G
+NC_000962.3	392261	snp	T	C
+NC_000962.3	393941	snp	C	T
+NC_000962.3	396750	snp	G	A
+NC_000962.3	403980	snp	G	A
+NC_000962.3	404326	snp	T	C
+NC_000962.3	406274	snp	T	C
+NC_000962.3	406599	snp	G	A
+NC_000962.3	412280	snp	T	G
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