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changeset 1:5b3e360ae7f7 draft

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Uploaded
author iuc
date Tue, 28 Apr 2015 22:46:31 -0400
parents 33ded39275c3
children 42a473d89b08
files macros.xml seqtk_comp.xml seqtk_cutN.xml seqtk_dropse.xml seqtk_fqchk.xml seqtk_hety.xml seqtk_listhet.xml seqtk_mergefa.xml seqtk_mergepe.xml seqtk_mutfa.xml seqtk_randbase.xml seqtk_sample.xml seqtk_seq.xml seqtk_subseq.xml seqtk_trimfq.xml test-data/paired_dat.fq test-data/paired_dat1.fq test-data/paired_dat2.fq test-data/seqtk_comp.fa test-data/seqtk_comp.out test-data/seqtk_cutn.fa test-data/seqtk_cutn.out test-data/seqtk_dropse.fq test-data/seqtk_dropse.out test-data/seqtk_fqchk.fq test-data/seqtk_fqchk.out test-data/seqtk_hety.fa test-data/seqtk_hety.out test-data/seqtk_listhet.fa test-data/seqtk_listhet.out test-data/seqtk_mergefa.out test-data/seqtk_mergefa1.fa test-data/seqtk_mergefa2.fa test-data/seqtk_mergefa2.out test-data/seqtk_mutfa.fa test-data/seqtk_mutfa.out test-data/seqtk_mutfa.snp test-data/seqtk_randbase.fa test-data/seqtk_randbase.out test-data/seqtk_sample.fa test-data/seqtk_sample.out test-data/seqtk_seq.fa test-data/seqtk_seq_revcom.fa test-data/seqtk_subseq.fa test-data/seqtk_subseq.out test-data/seqtk_subseq_list.txt test-data/seqtk_trimfq.fq test-data/seqtk_trimfq_be.fq test-data/seqtk_trimfq_default.fq tool_dependencies.xml tool_test_output.json
diffstat 51 files changed, 1 insertions(+), 1193 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<macros>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="1.0-r75-dirty">seqtk</requirement>
-      <yield/>
-    </requirements>
-  </xml>
-  <token name="@WRAPPER_VERSION@">1.0-r75-dirty</token>
-  <xml name="stdio">
-    <stdio>
-      <!-- Anything other than zero is an error -->
-      <exit_code range="1:"/>
-      <exit_code range=":-1"/>
-      <!-- In case the return code has not been set propery check stderr too -->
-      <regex match="Error:"/>
-      <regex match="Exception:"/>
-    </stdio>
-  </xml>
-  <xml name="in_fq">
-    <param name="in_file" type="data" format="fastq" label="Input FASTQ file"/>
-  </xml>
-  <xml name="in_faq">
-    <param name="in_file" type="data" format="fasta,fastq" label="Input FASTA/Q file"/>
-  </xml>
-  <token name="@ATTRIBUTION@"><![CDATA[
-**Attribution**
-
-This Galaxy tool relies on the seqtk toolkit from  `lh3/seqtk
-<https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
-  ]]>
-  </token>
-</macros>
--- a/seqtk_comp.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
-  <description>get the nucleotide composition of FASTA/Q</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk comp
-#if $in_bed:
--r $in_bed
-#end if
-
-$in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
-
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
-      <output name="default" file="seqtk_comp.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Reports composition of fasta/fastq sequences. For an example sequence like
-
-::
-    >test0
-    ACTGACTGAA
-    >ambig_ref
-    ACGTCGTGTTVHDBN
-
-The seqtk tool will report:
-
-::
-
-    #chr       length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
-    test0      11     4  2  2  2  0  0  1  0    0   0   0
-    ambig_ref  15     1  2  3  4  0  4  1  4    0   0   0
-
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_cutN.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
-  <description>cut sequence at long N</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk cutN -n $n
--p $p
-$g
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
-    <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
-    <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_cutn.fa"/>
-      <param name="n" value="1"/>
-      <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Splits long sequences with runs of Ns
-
-::
-
-    >test
-    AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
-This will be split into the component sequences without the ambiguity.
-
-::
-
-    >test:1-17
-    AACTGATCGATCGATCG
-    >test:29-33
-    ACATG
-
-
-@ATTRIBUTION@
-      ]]></help>
-</tool>
--- a/seqtk_dropse.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
-  <description>drop unpaired from interleaved Paired End FASTA/Q</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk dropse
-      $in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Only paired-end reads from $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_dropse.fq"/>
-      <output name="default" file="seqtk_dropse.out" ftype="fastq"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:
-
-::
-
-    @test-6/1
-    AGCTTGACGC
-    +
-    ?.HCF@C>>F
-    @test-6/2
-    TGCGAAGACC
-    +
-    >2?A?A@@7?
-    @test-4/1
-    CTTGACGCTG
-    +
-    I@>3EFCG@C
-    @test-2/1
-    AGACCAAAAT
-    +
-    ??><6E?IFC
-    @test-2/2
-    CTGGCGAATT
-    +
-    ?=?*?A?<?@
-
-This tool will remove the offending reads (test-4/1), leaving just the paired data.
-
-::
-
-    @test-6/1
-    AGCTTGACGC
-    +
-    ?.HCF@C>>F
-    @test-6/2
-    TGCGAAGACC
-    +
-    >2?A?A@@7?
-    @test-2/1
-    AGACCAAAAT
-    +
-    ??><6E?IFC
-    @test-2/2
-    CTGGCGAATT
-    +
-    ?=?*?A?<?@
-
-
-@ATTRIBUTION@
-      ]]></help>
-</tool>
--- a/seqtk_fqchk.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
-  <description>fastq QC (base/quality summary)</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk fqchk
--q $q
-$in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
-> $default]]></command>
-  <inputs>
-    <expand macro="in_fq"/>
-    <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_fqchk.fq"/>
-      <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Returns quality score information base-by-base.
-
-::
-
-    @SEQ_ID1
-    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-    +
-    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
-
-each based is examined individually and information reported:
-
-::
-
-    #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
-    #POS  #bases  %A     %C    %G     %T     %N   avgQ  errQ  %low   %high
-    #ALL  60      31.7   16.7  18.3   33.3   0.0  15.1  8.7   66.7   33.3
-    1     1       0.0    0.0   100.0  0.0    0.0  0.0   3.0   100.0  0.0
-    2     1       100.0  0.0   0.0    0.0    0.0  6.0   6.0   100.0  0.0
-    3     1       0.0    0.0   0.0    100.0  0.0  6.0   6.0   100.0  0.0
-    4     1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0
-    5     1       0.0    0.0   0.0    100.0  0.0  7.0   7.0   100.0  0.0
-    6     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
-    7     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
-    8     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
-    9     1       0.0    0.0   100.0  0.0    0.0  9.0   9.0   100.0  0.0
-    10    1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_hety.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0">
-  <description>regional heterozygosity</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk hety -w $w
--t $t
-$m
-$in_file | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="window size" help="(-w)" name="w" type="integer" value="50000"/>
-    <param label="# start positions in a window" help="(-t)" name="t" type="integer" value="5"/>
-    <param checked="false" label="treat lowercases as masked" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Heterozygous regions in $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_hety.fa"/>
-      <param name="w" value="8"/>
-      <output name="default" file="seqtk_hety.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Reports on heterozygosity over a region
-
-::
-
-    >het_region
-    ACTTTACATCGAGCMMMMMMMACAGTACTG
-
-As can be seen in the following output:
-
-::
-
-    #chr        start  end  A       B   num_het
-    het_region  0      8    0.00    8   0
-    het_region  8      9    0.00    8   0
-    het_region  9      10   0.00    8   0
-    het_region  10     11   0.00    8   0
-    het_region  11     12   0.00    8   0
-    het_region  12     13   0.00    8   0
-    het_region  13     14   0.00    8   0
-    het_region  14     15   1.00    8   1
-    het_region  15     16   2.00    8   2
-    het_region  16     17   3.00    8   3
-    het_region  17     18   4.00    8   4
-    het_region  18     19   5.00    8   5
-    het_region  19     20   6.00    8   6
-    het_region  20     21   7.00    8   7
-    het_region  21     22   7.00    8   7
-    het_region  22     23   6.00    8   6
-    het_region  23     24   5.00    8   5
-    het_region  24     25   4.00    8   4
-    het_region  25     26   3.00    8   3
-    het_region  26     27   2.00    8   2
-    het_region  27     28   1.00    8   1
-    het_region  28     29   0.00    8   0
-    het_region  29     30   0.00    1   0
-
-If you know what A and B are measures of, please `submit an issue <https://github.com/galaxyproject/tools-iuc/issues>`__ and it will be corrected
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_listhet.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_listhet" name="seqtk_listhet" version="@WRAPPER_VERSION@.0">
-  <description>extract the position of each het</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk listhet $in_file  | awk 'BEGIN{print "#chr\tposition\tbase"}1' > $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Positions of heterozygous bases in $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_listhet.fa"/>
-      <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Lists regions of heterozygosity.
-
-::
-
-    >ambig
-    ACGTMRWSYKVHDBN
-
-The seqtk suite recognises MRWSYK:
-
-::
-
-    #chr    position  base
-    ambig   5         M
-    ambig   6         R
-    ambig   7         W
-    ambig   8         S
-    ambig   9         Y
-    ambig   10        K
-
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_mergefa.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
-  <description>merge two FASTA/Q files</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk mergefa -q $q
-$i
-$m
-$r
-$h
-
-$in_fa1
-$in_fa2
-
-> $default]]></command>
-  <inputs>
-    <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-    <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
-    <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/>
-    <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/>
-    <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
-    <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
-    <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
-      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
-      <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
-    </test>
-    <test>
-      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
-      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
-      <param name="m" value="True" />
-      <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Merges two fasta files, using ambiguity codes
-
-::
-
-    # seq1.fa
-    >test0
-    ACTGACTGAAA
-
-    # seq2.fa
-    >test0
-    ACTGAMTGCGN
-
-In the following the `-m` option has been set to highlight seqtk-mergefa's features.
-
-::
-
-    >test0
-    ACTGACTGxxa
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_mergepe.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
-  <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk mergepe
-      $in_fq1
-      $in_fq2
-> $default]]></command>
-  <inputs>
-    <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-    <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
-  </inputs>
-  <outputs>
-      <data format_source="in_fq1" hidden="false" name="default" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_fq1" value="paired_dat1.fq"/>
-      <param name="in_fq2" value="paired_dat2.fq"/>
-      <output name="default" file="paired_dat.fq" ftype="fastq"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
-
-::
-
-    # r1.fq
-    @test-6/1
-    AGCTTGACGC
-    +
-    ?.HCF@C>>F
-
-    # r2.fq
-    @test-6/2
-    TGCGAAGACC
-    +
-    >2?A?A@@7?
-
-will produce the following paired file:
-
-::
-
-    @test-6/1
-    AGCTTGACGC
-    +
-    ?.HCF@C>>F
-    @test-6/2
-    TGCGAAGACC
-    +
-    >2?A?A@@7?
-
-While this may not have been an illuminating example, it is important to note
-that this tool will properly interleave data. For example if you have the ids:
-
-::
-
-    @r-1/1
-    @r-2/1
-    @r-3/1
-    @r-4/1
-
-and
-
-::
-
-    @r-1/2
-    @r-2/2
-    @r-3/2
-    @r-4/2
-
-These will be interleaved as
-
-::
-
-    @r-1/1
-    @r-1/2
-    @r-2/1
-    @r-2/2
-    @r-3/1
-    @r-3/2
-    @r-4/1
-    @r-4/2
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_mutfa.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
-  <description>point mutate FASTA at specified positions</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk mutfa
-      $in_file $in_snp
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_mutfa.fa"/>
-      <param name="in_snp" value="seqtk_mutfa.snp"/>
-      <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
-
-::
-
-    # Input fasta
-    >test0
-    ACTGACTGAA
-
-    # Input SNP file
-    test0 1 . G
-    test0 4 . A
-
-This will effect the desired mutations in the output file
-
-::
-
-    # Output result
-    >test0
-    GCTAACTGAA
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_randbase.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_randbase" name="seqtk_randbase" version="@WRAPPER_VERSION@.0">
-  <description>choose a random base from hets</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk randbase
-      $in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Unambiguous $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_randbase.fa"/>
-      <output name="default" file="seqtk_randbase.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Randomly resolves ambiguous bases
-
-::
-
-    # Input fasta
-    >ambig
-    ACGTMRWSYK
-
-results in
-
-::
-
-    # Output result
-    >ambig
-    ACGTCGTGTT
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_sample.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
-    <description>random subsample of fasta or fastq sequences</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk sample -s $s
-      $in_file
-      $subsample_size
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq" />
-    <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
-    <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_sample.fa"/>
-      <param name="subsample_size" value="4"/>
-      <param name="s" value="4"/>
-      <output name="default" file="seqtk_sample.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
-
-The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_seq.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0">
-  <description>common transformation of FASTA/Q</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk seq -q $q
--X $X
-#if $n and $n != "None" and $n is not None and $n != "":
--n "$n"
-#end if
--l $l
--Q $Q
--s $s
--f $f
-#if $M and $M != "None" and $M is not None and $M != "":
--M "$M"
-#end if
--L $L
-$c
-$r
-$A
-$C
-$N
-$x1
-$x2
-$V
-
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/>
-    <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/>
-    <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/>
-    <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/>
-    <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/>
-    <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/>
-    <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/>
-    <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/>
-    <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/>
-    <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/>
-    <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
-    <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/>
-    <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/>
-    <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
-    <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
-    <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
-    <param checked="false" label="shift quality by '(-Q) - 33' " help="(-V)" name="V" type="boolean" falsevalue="" truevalue="-V"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default"/>
-  </outputs>
-  <tests>
-    <test>
-      <!-- This is a sorry excuse for a test for a tool which does way more
-           than it should, but upstream decided to put a TON of functionality
-           into a single tool rather than using the single responsibility
-           principle. -->
-      <param name="in_file" value="seqtk_seq.fa"/>
-      <param name="r" value="True"/>
-      <param name="n" value=""/>
-      <param name="M" value=""/>
-      <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Various utilities for transforming FASTA/Q data
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_subseq.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
-  <description>extract subsequences from FASTA/Q files</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk subseq $t
--l $l
-$in_file
-
-#if $source.type == 'bed':
-  $in_bed
-#else
-  $name_list
-#end if
-
-#if $t == '-t':
- | awk 'BEGIN{print "chr\tunknown\tseq"}1'
-#end if
-
-> $default]]></command>
-  <inputs>
-    <param name="in_file" type="data" format="fasta,fastq" label="Input fasta/q file"/>
-    <conditional name="source">
-      <param name="type" type="select" label="Select source of sequence choices">
-        <option value="bed">BED</option>
-        <option value="name">FASTA/Q ID list</option>
-      </param>
-      <when value="bed">
-        <param name="in_bed" type="data" format="bed" label="Input BED file"/>
-      </when>
-      <when value="name">
-        <param name="name_list" type="data" format="txt" label="Input fasta file"/>
-      </when>
-    </conditional>
-    <param label="TAB delimited output" help="(-t)" name="t" type="boolean" falsevalue="" truevalue="-t"/>
-    <param label="sequence line length" help="(-l)" name="l" type="integer" value="0"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Selected sequences from $in_file.name">
-      <change_format>
-        <when input="t" value="-t" format="tabular"/>
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_subseq.fa"/>
-      <param name="type" value="name"/>
-      <param name="t" value="False" />
-      <param name="name_list" value="seqtk_subseq_list.txt"/>
-      <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
-
-::
-
-    # Input ID list
-    seq1
-
-    # Input fasta
-    >seq1
-    ACGTMRWSYK
-    >seq2
-    RWSYKACGTM
-
-results in
-
-::
-
-    # Output result
-    >seq1
-    ACGTMRWSYK
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/seqtk_trimfq.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-<?xml version="1.0"?>
-<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
-  <description>trim FASTQ using the Phred algorithm</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk trimfq
-#if $mode.mode_select == "quality":
--q $mode.q
--l $mode.l
-#else:
--b $mode.b
--e $mode.e
-#end if
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <conditional name="mode">
-        <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
-            <option value="quality">Quality</option>
-            <option value="position">Length/Position</option>
-        </param>
-        <when value="quality">
-            <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/>
-            <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/>
-        </when>
-        <when value="position">
-            <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/>
-            <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/>
-        </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_trimfq.fq"/>
-      <param name="mode_select" value="quality"/>
-      <param name="q" value="0.05"/>
-      <param name="l" value="30"/>
-      <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
-    </test>
-    <test>
-      <param name="in_file" value="seqtk_trimfq.fq"/>
-      <param name="mode_select" value="position"/>
-      <param name="b" value="5"/>
-      <param name="e" value="5"/>
-      <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Trim a fastq file based on Phred scores, or by length
-
-@ATTRIBUTION@
-]]></help>
-</tool>
--- a/test-data/paired_dat.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/1
-CTTGACGCTG
-+
-I@>3EFCG@C
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@<BC
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?<?@
--- a/test-data/paired_dat1.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-4/1
-CTTGACGCTG
-+
-I@>3EFCG@C
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
--- a/test-data/paired_dat2.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@<BC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?<?@
--- a/test-data/seqtk_comp.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
->test0
-ACTGACTGAA
->ambig_ref
-ACGTCGTGTTVHDBN
-
--- a/test-data/seqtk_comp.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#chr	length	#A	#C	#G	#T	#2	#3	#4	#CpG	#tv	#ts	#CpG-ts
-test0	10	4	2	2	2	0	0	0	0	0	0	0
-ambig_ref	15	1	2	3	4	0	4	1	4	0	0	0
--- a/test-data/seqtk_cutn.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->test
-AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
--- a/test-data/seqtk_cutn.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->test:1-17
-AACTGATCGATCGATCG
->test:29-33
-ACATG
--- a/test-data/seqtk_dropse.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@<BC
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?<?@
--- a/test-data/seqtk_dropse.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?<?@
--- a/test-data/seqtk_fqchk.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
--- a/test-data/seqtk_fqchk.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
-#POS	#bases	%A	%C	%G	%T	%N	avgQ	errQ	%low	%high
-#ALL	60	31.7	16.7	18.3	33.3	0.0	15.1	8.7	66.7	33.3
-1	1	0.0	0.0	100.0	0.0	0.0	0.0	3.0	100.0	0.0
-2	1	100.0	0.0	0.0	0.0	0.0	6.0	6.0	100.0	0.0
-3	1	0.0	0.0	0.0	100.0	0.0	6.0	6.0	100.0	0.0
-4	1	0.0	0.0	0.0	100.0	0.0	9.0	9.0	100.0	0.0
-5	1	0.0	0.0	0.0	100.0	0.0	7.0	7.0	100.0	0.0
-6	1	0.0	0.0	100.0	0.0	0.0	7.0	7.0	100.0	0.0
-7	1	0.0	0.0	100.0	0.0	0.0	7.0	7.0	100.0	0.0
-8	1	0.0	0.0	100.0	0.0	0.0	7.0	7.0	100.0	0.0
-9	1	0.0	0.0	100.0	0.0	0.0	9.0	9.0	100.0	0.0
-10	1	0.0	0.0	0.0	100.0	0.0	9.0	9.0	100.0	0.0
-11	1	0.0	0.0	0.0	100.0	0.0	9.0	9.0	100.0	0.0
-12	1	0.0	100.0	0.0	0.0	0.0	10.0	10.0	100.0	0.0
-13	1	100.0	0.0	0.0	0.0	0.0	8.0	8.0	100.0	0.0
-14	1	100.0	0.0	0.0	0.0	0.0	8.0	8.0	100.0	0.0
-15	1	100.0	0.0	0.0	0.0	0.0	4.0	4.0	100.0	0.0
-16	1	0.0	0.0	100.0	0.0	0.0	4.0	4.0	100.0	0.0
-17	1	0.0	100.0	0.0	0.0	0.0	4.0	4.0	100.0	0.0
-18	1	100.0	0.0	0.0	0.0	0.0	10.0	10.0	100.0	0.0
-19	1	0.0	0.0	100.0	0.0	0.0	10.0	10.0	100.0	0.0
-20	1	0.0	0.0	0.0	100.0	0.0	8.0	8.0	100.0	0.0
-21	1	100.0	0.0	0.0	0.0	0.0	7.0	7.0	100.0	0.0
-22	1	0.0	0.0	0.0	100.0	0.0	4.0	4.0	100.0	0.0
-23	1	0.0	100.0	0.0	0.0	0.0	4.0	4.0	100.0	0.0
-24	1	0.0	0.0	100.0	0.0	0.0	4.0	4.0	100.0	0.0
-25	1	100.0	0.0	0.0	0.0	0.0	4.0	4.0	100.0	0.0
-26	1	0.0	0.0	0.0	100.0	0.0	8.0	8.0	100.0	0.0
-27	1	0.0	100.0	0.0	0.0	0.0	13.0	13.0	100.0	0.0
-28	1	100.0	0.0	0.0	0.0	0.0	16.0	16.0	100.0	0.0
-29	1	100.0	0.0	0.0	0.0	0.0	9.0	9.0	100.0	0.0
-30	1	100.0	0.0	0.0	0.0	0.0	9.0	9.0	100.0	0.0
-31	1	0.0	0.0	0.0	100.0	0.0	9.0	9.0	100.0	0.0
-32	1	100.0	0.0	0.0	0.0	0.0	12.0	12.0	100.0	0.0
-33	1	0.0	0.0	100.0	0.0	0.0	10.0	10.0	100.0	0.0
-34	1	0.0	0.0	0.0	100.0	0.0	9.0	9.0	100.0	0.0
-35	1	100.0	0.0	0.0	0.0	0.0	6.0	6.0	100.0	0.0
-36	1	100.0	0.0	0.0	0.0	0.0	6.0	6.0	100.0	0.0
-37	1	100.0	0.0	0.0	0.0	0.0	8.0	8.0	100.0	0.0
-38	1	0.0	0.0	0.0	100.0	0.0	8.0	8.0	100.0	0.0
-39	1	0.0	100.0	0.0	0.0	0.0	9.0	9.0	100.0	0.0
-40	1	0.0	100.0	0.0	0.0	0.0	9.0	9.0	100.0	0.0
-41	1	100.0	0.0	0.0	0.0	0.0	20.0	20.0	0.0	100.0
-42	1	0.0	0.0	0.0	100.0	0.0	20.0	20.0	0.0	100.0
-43	1	0.0	0.0	0.0	100.0	0.0	34.0	34.0	0.0	100.0
-44	1	0.0	0.0	0.0	100.0	0.0	34.0	34.0	0.0	100.0
-45	1	0.0	0.0	100.0	0.0	0.0	37.0	37.0	0.0	100.0
-46	1	0.0	0.0	0.0	100.0	0.0	29.0	29.0	0.0	100.0
-47	1	0.0	0.0	0.0	100.0	0.0	29.0	29.0	0.0	100.0
-48	1	0.0	100.0	0.0	0.0	0.0	29.0	29.0	0.0	100.0
-49	1	100.0	0.0	0.0	0.0	0.0	29.0	29.0	0.0	100.0
-50	1	100.0	0.0	0.0	0.0	0.0	29.0	29.0	0.0	100.0
-51	1	0.0	100.0	0.0	0.0	0.0	29.0	29.0	0.0	100.0
-52	1	0.0	0.0	0.0	100.0	0.0	34.0	34.0	0.0	100.0
-53	1	0.0	100.0	0.0	0.0	0.0	34.0	34.0	0.0	100.0
-54	1	100.0	0.0	0.0	0.0	0.0	34.0	34.0	0.0	100.0
-55	1	0.0	100.0	0.0	0.0	0.0	34.0	34.0	0.0	100.0
-56	1	100.0	0.0	0.0	0.0	0.0	34.0	34.0	0.0	100.0
-57	1	0.0	0.0	100.0	0.0	0.0	34.0	34.0	0.0	100.0
-58	1	0.0	0.0	0.0	100.0	0.0	34.0	34.0	0.0	100.0
-59	1	0.0	0.0	0.0	100.0	0.0	21.0	21.0	0.0	100.0
-60	1	0.0	0.0	0.0	100.0	0.0	20.0	20.0	0.0	100.0
--- a/test-data/seqtk_hety.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->het_region
-ACTTTACATCGAGCMMMMMMMACAGTACTG
-
--- a/test-data/seqtk_hety.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-#chr	start	end	A	B	num_het
-het_region	0	8	0.00	8	0
-het_region	8	9	0.00	8	0
-het_region	9	10	0.00	8	0
-het_region	10	11	0.00	8	0
-het_region	11	12	0.00	8	0
-het_region	12	13	0.00	8	0
-het_region	13	14	0.00	8	0
-het_region	14	15	1.00	8	1
-het_region	15	16	2.00	8	2
-het_region	16	17	3.00	8	3
-het_region	17	18	4.00	8	4
-het_region	18	19	5.00	8	5
-het_region	19	20	6.00	8	6
-het_region	20	21	7.00	8	7
-het_region	21	22	7.00	8	7
-het_region	22	23	6.00	8	6
-het_region	23	24	5.00	8	5
-het_region	24	25	4.00	8	4
-het_region	25	26	3.00	8	3
-het_region	26	27	2.00	8	2
-het_region	27	28	1.00	8	1
-het_region	28	29	0.00	8	0
-het_region	29	30	0.00	1	0
--- a/test-data/seqtk_listhet.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->ambig
-ACGTMRWSYKVHDBN
-
--- a/test-data/seqtk_listhet.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#chr	position	base
-ambig	5	M
-ambig	6	R
-ambig	7	W
-ambig	8	S
-ambig	9	Y
-ambig	10	K
--- a/test-data/seqtk_mergefa.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGAMTGMRN
--- a/test-data/seqtk_mergefa1.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGAAA
--- a/test-data/seqtk_mergefa2.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGAMTGCGN
--- a/test-data/seqtk_mergefa2.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGxxa
--- a/test-data/seqtk_mutfa.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGAA
--- a/test-data/seqtk_mutfa.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-GCTAACTGAA
--- a/test-data/seqtk_mutfa.snp	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-test0 1 . G
-test0 4 . A
--- a/test-data/seqtk_randbase.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->ambig
-ACGTMRWSYK
--- a/test-data/seqtk_randbase.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->ambig
-ACGTCGTGTT
--- a/test-data/seqtk_sample.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
->seq0
-AAAAAAAAAA
-AAAAAAAAAA
->seq1
-TTTTTTTTTT
-TTTTTTTTTT
->seq2
-CCCCCCCCCC
-CCCCCCCCCC
->seq3
-GGGGGGGGGG
-GGGGGGGGGG
->seq4
-AAAAAAAAAA
-TTTTTTTTTT
->seq5
-AAAAAAAAAA
-CCCCCCCCCC
->seq6
-AAAAAAAAAA
-GGGGGGGGGG
->seq7
-TTTTTTTTTT
-CCCCCCCCCC
->seq8
-TTTTTTTTTT
-GGGGGGGGGG
--- a/test-data/seqtk_sample.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->seq7
-TTTTTTTTTTCCCCCCCCCC
->seq1
-TTTTTTTTTTTTTTTTTTTT
->seq4
-AAAAAAAAAATTTTTTTTTT
->seq3
-GGGGGGGGGGGGGGGGGGGG
--- a/test-data/seqtk_seq.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->test
-AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
--- a/test-data/seqtk_seq_revcom.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test
-CATGTNNNNNNNNNNNCGATCGATCGATCAGTT
--- a/test-data/seqtk_subseq.fa	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->seq1
-ACGTMRWSYK
->seq2
-RWSYKACGTM
--- a/test-data/seqtk_subseq.out	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->seq1
-ACGTMRWSYK
--- a/test-data/seqtk_subseq_list.txt	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-seq1
--- a/test-data/seqtk_trimfq.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
--- a/test-data/seqtk_trimfq_be.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC
-+
-(((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCC
--- a/test-data/seqtk_trimfq_default.fq	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-TAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-*-+*''))**55CCF>>>>>>CCCCCCC65
--- a/tool_dependencies.xml	Wed Feb 18 10:52:53 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="seqtk" version="1.0-r75-dirty">
-    <repository changeset_revision="f059064a6de2" name="package_seqtk_1_0_r75" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_test_output.json	Tue Apr 28 22:46:31 2015 -0400
@@ -0,0 +1,1 @@
+{"tests": [{"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "job": {"inputs": {"in_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-02-18T11:43:38.160465", "tool_id": "seqtk_comp", "outputs": {"default": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "seqtk comp  /tmp/tmpjaBvNBfiles/000/dataset_1.dat | awk 'BEGIN{print \"#chr\\tlength\\t#A\\t#C\\t#G\\t#T\\t#2\\t#3\\t#4\\t#CpG\\t#tv\\t#ts\\t#CpG-ts\"}1'  > /tmp/tmpjaBvNBfiles/000/dataset_2.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:43:33.442909", "params": {"in_bed": "null", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1409", "id": "5729865256bc2525", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_comp.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "54f2a3a23292eb07"}, "n": "1"}, "job": {"inputs": {"in_file": {"src": "hda", "id": "54f2a3a23292eb07"}}, "update_time": "2015-02-18T11:43:53.292491", "tool_id": "seqtk_cutN", "outputs": {"default": {"src": "hda", "id": "8155e4b4bf1581ff"}}, "stdout": "", "command_line": "seqtk cutN -n 1 -p 10  /tmp/tmpjaBvNBfiles/000/dataset_3.dat > /tmp/tmpjaBvNBfiles/000/dataset_4.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:43:48.995235", "params": {"p": "\"10\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "g": "\"False\"", "n": "\"1\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1430", "id": "8155e4b4bf1581ff", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_cutN.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "7b55dbb89df8f4e5"}}, "job": {"inputs": {"in_file": {"src": "hda", "id": "7b55dbb89df8f4e5"}}, "update_time": "2015-02-18T11:44:13.507868", "tool_id": "seqtk_dropse", "outputs": {"default": {"src": "hda", "id": "fa6d20d0fb68383f"}}, "stdout": "", "command_line": "seqtk dropse /tmp/tmpjaBvNBfiles/000/dataset_5.dat > /tmp/tmpjaBvNBfiles/000/dataset_6.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:44:09.075891", "params": {"chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1452", "id": "fa6d20d0fb68383f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_dropse.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "683bc220e21425bb"}}, "job": {"inputs": {"in_file": {"src": "hda", "id": "683bc220e21425bb"}}, "update_time": "2015-02-18T11:44:31.059619", "tool_id": "seqtk_fqchk", "outputs": {"default": {"src": "hda", "id": "a90a30fafe298e1e"}}, "stdout": "", "command_line": "seqtk fqchk -q 20 /tmp/tmpjaBvNBfiles/000/dataset_7.dat | awk '{if(NR<4){print \"#\"$0}else{print $0}}' > /tmp/tmpjaBvNBfiles/000/dataset_8.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:44:27.033199", "params": {"q": "\"20\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1472", "id": "a90a30fafe298e1e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_fqchk.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "b842d972534ccb3e"}, "w": "8"}, "job": {"inputs": {"in_file": {"src": "hda", "id": "b842d972534ccb3e"}}, "update_time": "2015-02-18T11:44:49.092882", "tool_id": "seqtk_hety", "outputs": {"default": {"src": "hda", "id": "5449172d6ff5669b"}}, "stdout": "", "command_line": "seqtk hety -w 8 -t 5  /tmp/tmpjaBvNBfiles/000/dataset_9.dat | awk 'BEGIN{print \"#chr\\tstart\\tend\\tA\\tB\\tnum_het\"}1' > /tmp/tmpjaBvNBfiles/000/dataset_10.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:44:43.403095", "params": {"chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "m": "\"False\"", "t": "\"5\"", "w": "\"8\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1493", "id": "5449172d6ff5669b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_hety.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "9ce08b2254e4d5ed"}}, "job": {"inputs": {"in_file": {"src": "hda", "id": "9ce08b2254e4d5ed"}}, "update_time": "2015-02-18T11:45:03.232698", "tool_id": "seqtk_listhet", "outputs": {"default": {"src": "hda", "id": "80b8022ff3f677b7"}}, "stdout": "", "command_line": "seqtk listhet /tmp/tmpjaBvNBfiles/000/dataset_11.dat  | awk 'BEGIN{print \"#chr\\tposition\\tbase\"}1' > /tmp/tmpjaBvNBfiles/000/dataset_12.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:44:58.854932", "params": {"chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1514", "id": "80b8022ff3f677b7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_listhet.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"in_fa2": {"src": "hda", "id": "1ae74d26531588b0"}, "in_fa1": {"src": "hda", "id": "b54fb481e575bccc"}}, "job": {"inputs": {"in_fa2": {"src": "hda", "id": "1ae74d26531588b0"}, "in_fa1": {"src": "hda", "id": "b54fb481e575bccc"}}, "update_time": "2015-02-18T11:45:30.017193", "tool_id": "seqtk_mergefa", "outputs": {"default": {"src": "hda", "id": "440a6c2b5d9efe20"}}, "stdout": "", "command_line": "seqtk mergefa -q 0      /tmp/tmpjaBvNBfiles/000/dataset_13.dat /tmp/tmpjaBvNBfiles/000/dataset_14.dat  > /tmp/tmpjaBvNBfiles/000/dataset_15.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:45:25.868594", "params": {"i": "\"False\"", "h": "\"False\"", "m": "\"False\"", "dbkey": "\"hg17\"", "q": "\"0\"", "r": "\"False\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "[stk_mergefa] (same,diff,hom-het,het-hom,het-het)=(7,2,1,0,0)\n", "job_metrics": [], "model_class": "Job", "external_id": "1546", "id": "440a6c2b5d9efe20", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_mergefa.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"m": "True", "in_fa2": {"src": "hda", "id": "27ee89e2e3d631e0"}, "in_fa1": {"src": "hda", "id": "ea0b941dfbe636f8"}}, "job": {"inputs": {"in_fa2": {"src": "hda", "id": "27ee89e2e3d631e0"}, "in_fa1": {"src": "hda", "id": "ea0b941dfbe636f8"}}, "update_time": "2015-02-18T11:45:55.971535", "tool_id": "seqtk_mergefa", "outputs": {"default": {"src": "hda", "id": "61f03d5eef6f1538"}}, "stdout": "", "command_line": "seqtk mergefa -q 0  -m    /tmp/tmpjaBvNBfiles/000/dataset_16.dat /tmp/tmpjaBvNBfiles/000/dataset_17.dat  > /tmp/tmpjaBvNBfiles/000/dataset_18.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:45:51.174795", "params": {"i": "\"False\"", "h": "\"False\"", "m": "\"True\"", "dbkey": "\"hg17\"", "q": "\"0\"", "r": "\"False\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "[stk_mergefa] (same,diff,hom-het,het-hom,het-het)=(7,2,1,0,0)\n", "job_metrics": [], "model_class": "Job", "external_id": "1577", "id": "61f03d5eef6f1538", "user_email": "test@bx.psu.edu"}}, "id": 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\ No newline at end of file