umi_tools_count: macros.xml annotate

annotate macros.xml @ 8:e654095ab143 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"

author	iuc
date	Mon, 13 Sep 2021 14:49:44 +0000
parents	933220bbc2ae
children	24013bf85a6f

rev	line source
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	1 <?xml version="1.0"?>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	2 <macros>
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	3
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	4 <!-- macros applying to all umi_tools -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	5
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	6 <token name="@TOOL_VERSION@">1.1.2</token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	7 <token name="@VERSION_SUFFIX@">0</token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	8 <token name="@PROFILE@">21.01</token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	9 <xml name="requirements">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	10 <requirements>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	12 <yield />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	13 </requirements>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	14 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	15 <xml name="citations">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	16 <citations>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	17 <citation type="doi">10.1101/gr.209601.116</citation>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	18 <citation type="bibtex">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	19 @misc{githubUMI-tools,
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	20 title = {UMI-tools},
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	21 publisher = {GitHub},
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	22 journal = {GitHub repository},
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	23 url = {https://github.com/CGATOxford/UMI-tools},
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	24 }
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	25 </citation>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	26 </citations>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	27 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	28 <xml name="advanced_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	29 <section name="advanced" title="Extra parameters" expanded="false">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	30 <param argument="--random-seed" type="integer" min="0" optional="true" label="Random Seed" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	31 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	32 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	33 <token name="@ADVANCED_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	34 #if str($advanced.random_seed) != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	35 --random-seed='$advanced.random_seed'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	36 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	37 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	38
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	39 <!-- macros for extract and whitelist-->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	40
4 70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	41 <macro name="barcode_sanitizer" >
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	42 <sanitizer invalid_char="">
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	43 <valid initial="string.letters,string.digits">
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	44 <add value="*" /><!-- asterisk -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	45 <add value="," /><!-- comma -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	46 <add value="." /><!-- period -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	47 <add value="<" /><!-- less than -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	48 <add value="=" /><!-- equals sign -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	49 <add value=">" /><!-- greater than -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	50 <add value="?" /><!-- question mark -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	51 <add value="_" /><!-- underscore -->
5 933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	52 <add value="(" /><!-- left bracket -->
933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	53 <add value=")" /><!-- right bracket -->
933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	54 <add value="["/> <!-- left square bracket -->
933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	55 <add value="]"/> <!-- right square bracket -->
4 70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	56 <add value="{"/><!-- left brace -->
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	57 <add value="}"/><!-- right brace -->
5 933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	58 <add value="^"/> <!-- caret -->
933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	59 <add value="-"/>
933220bbc2ae "planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f" iuc parents: 4 diff changeset	60 <add value="!"/>
4 70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	61 </valid>
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	62 </sanitizer>
70cb5527defb "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" iuc parents: 0 diff changeset	63 </macro>
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	64 <xml name="sanitize_tag" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	65 <sanitizer invalid_char="">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	66 <valid initial="string.letters,string.digits" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	67 </sanitizer>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	68 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	69 <macro name="barcode1_macro" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	70 <param argument="--bc-pattern" type="text" label="Barcode pattern for first read"
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	71 help="Use this option to specify the format of the UMI/barcode. Use Ns to
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	72 represent the random positions and Xs to indicate the bc positions.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	73 Bases with Ns will be extracted and added to the read name. Remaining
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	74 bases, marked with an X will be reattached to the read">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	75 <validator type="empty_field" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	76 <expand macro="barcode_sanitizer" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	77 </param>
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	78 </macro>
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	79 <macro name="barcode2_macro" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	80 <param argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	81 help="Use this option to specify the format of the UMI/barcode for
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	82 the second read pair if required" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	83 <expand macro="barcode_sanitizer" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	84 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	85 </macro>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	86 <!-- not just fastq because this would allow also fastqcsanger -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	87 <token name="@FASTQ_FORMATS@">fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz</token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	88 <xml name="bio_tools">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	89 <xrefs>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	90 <xref type="bio.tools">umi-tools</xref>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	91 </xrefs>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	92 </xml>
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	93 <xml name="input_types">
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	94 <conditional name="input_type_cond">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	95 <param name="input_type" type="select" label="Library type">
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	96 <option value="single">Single-end</option>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	97 <option value="paired">Paired-end</option>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	98 <option value="paired_collection">Paired-end Dataset Collection</option>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	99 </param>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	100 <when value="single">
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	101 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	102 <expand macro="barcode1_macro"/>
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	103 </when>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	104 <when value="paired">
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	105 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	106 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	107 <expand macro="barcode1_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	108 <expand macro="barcode2_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	109 <yield/>
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	110 </when>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	111 <when value="paired_collection">
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	112 <param name="input_readpair" type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	113 <expand macro="barcode1_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	114 <expand macro="barcode2_macro"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	115 <yield/>
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	116 </when>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	117 </conditional>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	118 </xml>
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	119 <token name="@COMMAND_LINK@"><![CDATA[
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	120 #set $gz = False
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	121 #if $input_type_cond.input_type == 'single':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	122 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	123 ln -s '$input_type_cond.input_read1' input_single.gz &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	124 #set $gz = True
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	125 #else
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	126 ln -s '$input_type_cond.input_read1' input_single.txt &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	127 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	128 #elif $input_type_cond.input_type == 'paired':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	129 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	130 ln -s '$input_type_cond.input_read1' input_read1.gz &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	131 ln -s '$input_type_cond.input_read2' input_read2.gz &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	132 #set $gz = True
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	133 #else
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	134 ln -s '$input_type_cond.input_read1' input_read1.txt &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	135 ln -s '$input_type_cond.input_read2' input_read2.txt &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	136 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	137 #else ## paired_collection
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	138 #if $input_type_cond.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	139 ln -s '$input_type_cond.input_readpair.forward' input_read1.gz &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	140 ln -s '$input_type_cond.input_readpair.reverse' input_read2.gz &&
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	141 #set $gz = True
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	142 #else
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	143 ln -s '$input_type_cond.input_readpair.forward' input_read1.txt &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	144 ln -s '$input_type_cond.input_readpair.reverse' input_read2.txt &&
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	145 #end if
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	146 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	147 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	148
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	149 <!-- macros for count, dedup, and group -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	150
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	151 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	152 #if $input.is_of_type("sam"):
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	153 ## TODO dedup has problems with SAM input in some cases
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	154 ## https://github.com/CGATOxford/UMI-tools/issues/483
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	155 ## so convert it to sorted BAM for now
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	156 ## #set $input_file = $input
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	157 samtools sort --no-PG '$input' > 'input.bam' &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	158 samtools index -b 'input.bam' &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	159 #set $input_file = 'input.bam'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	160 #else:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	161 ln -sf '${input}' 'input.bam' &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	162 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	163 #set $input_file = 'input.bam'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	164 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	165 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	166 <token name="@SET_INPUT_TYPE@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	167 ## TODO see comment in LINK_SAM_BAM_INPUT
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	168 ## #if $input.is_of_type("sam"):
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	169 ## --in-sam
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	170 ## #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	171 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	172
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	173 <xml name="fastq_barcode_extraction_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	174 <conditional name="extract_method_cond">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	175 <param argument="--extract-method" type="select" label="Barcode Extraction Method"
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	176 help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	177 <option value="string" selected="true" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	178 <option value="regex" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	179 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	180 <when value="string">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	181 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	182 truevalue="--3prime" falsevalue=""
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	183 help="By default the barcode is assumed to be on the 5' end of the read, but
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	184 use this option to specify that it is on the 3' end instead.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	185 This option only works with ``--extract-method=string``
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	186 since 3' encoding can be specified explicitly with a regex, e.g
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	187 ``.*(?P<umi_1>.{5})$``" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	188 </when>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	189 <when value="regex">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	190 <param name="filtered_out_bool" type="boolean" label="Write out reads not matching regex pattern"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	191 </when>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	192 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	193 <param argument="--ignore-read-pair-suffixes" type="boolean" truevalue="--ignore-read-pair-suffixes" falsevalue="" label="Ignore '\1' and '\2' read name suffixes"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	194 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	195 <token name="@FASTQ_BARCODE_EXTRACTION_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	196 ## fastq barcode extraction options:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	197 --extract-method='$extract_method_cond.extract_method'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	198 --bc-pattern='$input_type_cond.bc_pattern'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	199 #if $input_type_cond.input_type != 'single' and $input_type_cond.bc_pattern2 != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	200 --bc-pattern2='$input_type_cond.bc_pattern2'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	201 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	202 #if $extract_method_cond.extract_method == 'string'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	203 $extract_method_cond.prime3
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	204 #else if $extract_method_cond.filtered_out_bool
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	205 #if $input_type_cond.input_type == 'single':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	206 --filtered-out='$filtered_out'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	207 #else if $input_type_cond.input_type == 'paired':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	208 --filtered-out='$filtered_out'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	209 --filtered-out2='$filtered_out_paired'
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	210 #else
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	211 --filtered-out='$filtered_out_paired_collection.forward'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	212 --filtered-out2='$filtered_out_paired_collection.reverse'
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	213 #end if
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	214 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	215 $ignore_read_pair_suffixes
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	216 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	217 <token name="@FASTQ_BARCODE_EXTRACTION_HELP@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	218 There are two methods enabled to extract the umi barcode (+/-
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	219 cell barcode). For both methods, the patterns should be provided
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	220 using the ``--bc-pattern`` and ``--bc-pattern2`` options.x
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	221
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	222 - ``string``
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	223 This should be used where the barcodes are always in the same
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	224 place in the read.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	225
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	226 - N = UMI position (required)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	227 - C = cell barcode position (optional)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	228 - X = sample position (optional)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	229
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	230 Bases with Ns and Cs will be extracted and added to the read
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	231 name. The corresponding sequence qualities will be removed from
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	232 the read. Bases with an X will be reattached to the read.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	233
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	234 E.g. If the pattern is `NNNNCC`,
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	235 Then the read::
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	236
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	237 @HISEQ:87:00000000 read1
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	238 AAGGTTGCTGATTGGATGGGCTAG
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	239 +
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	240 DA1AEBFGGCG01DFH00B1FF0B
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	241
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	242 will become::
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	243
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	244 @HISEQ:87:00000000_TT_AAGG read1
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	245 GCTGATTGGATGGGCTAG
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	246 +
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	247 1AFGGCG01DFH00B1FF0B
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	248
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	249 where 'TT' is the cell barcode and 'AAGG' is the UMI.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	250
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	251 - ``regex``
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	252 This method allows for more flexible barcode extraction and
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	253 should be used where the cell barcodes are variable in
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	254 length. Alternatively, the regex option can also be used to
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	255 filter out reads which do not contain an expected adapter
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	256 sequence. UMI-tools uses the regex module rather than the more
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	257 standard re module since the former also enables fuzzy matching
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	258
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	259 The regex must contain groups to define how the barcodes are
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	260 encoded in the read. The expected groups in the regex are:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	261
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	262 umi_n = UMI positions, where n can be any value (required)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	263 cell_n = cell barcode positions, where n can be any value (optional)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	264 discard_n = positions to discard, where n can be any value (optional)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	265
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	266 UMI positions and cell barcode positions will be extracted and
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	267 added to the read name. The corresponding sequence qualities
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	268 will be removed from the read.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	269
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	270 Discard bases and the corresponding quality scores will be
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	271 removed from the read. All bases matched by other groups or
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	272 components of the regex will be reattached to the read sequence
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	273
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	274 For example, the following regex can be used to extract reads
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	275 from the Klein et al inDrop data::
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	276
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	277 (?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT)(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.*
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	278
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	279 Where only reads with a 3' T-tail and `GAGTGATTGCTTGTGACGCCTT` in
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	280 the correct position to yield two cell barcodes of 8-12 and 8bp
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	281 respectively, and a 6bp UMI will be retained.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	282
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	283 You can also specify fuzzy matching to allow errors. For example if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	284 the discard group above was specified as below this would enable
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	285 matches with up to 2 errors in the discard_1 group.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	286
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	287 ::
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	288
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	289 (?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	290
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	291 Note that all UMIs must be the same length for downstream
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	292 processing with dedup, group or count commands]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	293
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	294 <xml name="barcode_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	295 <conditional name="bc" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	296 <param argument="--extract-umi-method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	297 <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	298 <option value="tag" >Barcodes are contained in tags</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	299 <option value="umis" >Barcodes were extracted using umis</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	300 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	301 <when value="read_id" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	302 <param argument="--umi-separator" type="text" label="Delimiter between read id and the UMI" value="_" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	303 <sanitizer invalid_char="" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	304 <valid initial="string.punctuation" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	305 </sanitizer>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	306 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	307 </when>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	308 <when value="tag" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	309 <param argument="--umi-tag" type="text" label="Tag which contains the UMI" value="RX" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	310 <expand macro="sanitize_tag" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	311 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	312 <param argument="--umi-tag-split" type="text" label="Separate the UMI in tag by SPLIT" help="and take the first element"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	313 <param argument="--umi-tag-delimiter" type="text" label="Separate the UMI in tag by DELIMITER" help="and concatenate the elements"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	314 <param argument="--cell-tag" type="text" label="Tag which contains the cell barcode" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	315 <expand macro="sanitize_tag" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	316 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	317 <param argument="--cell-tag-split" type="text" label="Separate the cell barcode in tag by SPLIT" help="and take the first element"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	318 <param argument="--cell-tag-delimiter" type="text" label="Separate the cell barcode in tag by DELIMITER" help="and concatenate the elements"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	319 </when>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	320 <when value="umis"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	321 </conditional>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	322 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	323 <token name="@BARCODE_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	324 --extract-umi-method $bc.extract_umi_method
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	325 #if str($bc.extract_umi_method) == 'read_id':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	326 --umi-separator '$bc.umi_separator'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	327 #else if str($bc.extract_umi_method) == 'tag':
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	328 --umi-tag '$bc.umi_tag'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	329 #if $bc.umi_tag_split != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	330 --umi-tag-split '$bc.umi_tag_split'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	331 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	332 #if $bc.umi_tag_delimiter != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	333 --umi-tag-delimiter '$bc.umi_tag_delimiter'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	334 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	335 --cell-tag '$bc.cell_tag'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	336 #if $bc.cell_tag_split != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	337 --cell-tag-split '$bc.cell_tag_split'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	338 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	339 #if $bc.cell_tag_delimiter != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	340 --cell-tag-delimiter '$bc.cell_tag_delimiter'
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	341 #end if
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	342 #end if
8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	343 ]]></token>
8 e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	344 <token name="@BARCODE_HELP@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	345 Extracting barcodes
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	346 -------------------
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	347
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	348 It is assumed that the FASTQ files were processed with ``umi_tools
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	349 extract`` before mapping and thus the UMI is the last word of the read
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	350 name. e.g:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	351
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	352 @HISEQ:87:00000000_AATT
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	353
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	354 where ``AATT`` is the UMI sequeuence.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	355
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	356 If you have used an alternative method which does not separate the
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	357 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	358 specify the separator with the option ``--umi-separator=<sep>``,
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	359 replacing <sep> with e.g ":".
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	360
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	361 Alternatively, if your UMIs are encoded in a tag, you can specify this
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	362 by setting the option --extract-umi-method=tag and set the tag name
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	363 with the --umi-tag option. For example, if your UMIs are encoded in
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	364 the 'UM' tag, provide the following options:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	365 ``--extract-umi-method=tag`` ``--umi-tag=UM``
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	366
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	367 Finally, if you have used umis to extract the UMI +/- cell barcode,
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	368 you can specify ``--extract-umi-method=umis``
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	369
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	370 The start position of a read is considered to be the start of its alignment
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	371 minus any soft clipped bases. A read aligned at position 500 with
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	372 cigar 2S98M will be assumed to start at position 498.]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	373
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	374
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	375 <xml name="umi_grouping_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	376 <section name="umi" title="UMI grouping options">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	377 <param argument="--method" type="select" label="Method used to identify PCR duplicates within reads" help="All methods start by identifying the reads with the same mapping position">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	378 <option value="unique">Reads group share the exact same UMI</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	379 <option value="percentile">Reads group share the exact same UMI. UMIs with counts less than 1% of the median counts for UMIs at the same position are ignored</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	380 <option value="cluster">Identify clusters based on hamming distance</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	381 <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	382 <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	383 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	384 <param argument="--edit-distance-threshold" type="integer" value="1" label="Edit distance threshold" help="For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (>14bp)" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	385 <param argument="--spliced-is-unique" type="boolean" truevalue="--spliced-is-unique" falsevalue="" label="Spliced reads are unique" help="Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation to test for splicing)" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	386 <param argument="--soft-clip-threshold" type="integer" value="4" label="Soft clip threshold" help="Mappers that soft clip, will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many bases soft-clipped at the 3' end as spliced" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	387 <param argument="--read-length" type="boolean" truevalue="--read-length" falsevalue="" label="Use the read length as as a criterion when deduping" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	388 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	389 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	390 <token name="@UMI_GROUPING_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	391 --method $umi.method
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	392 --edit-distance-threshold $umi.edit_distance_threshold
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	393 $umi.spliced_is_unique
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	394 --soft-clip-threshold $umi.soft_clip_threshold
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	395 $umi.read_length
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	396 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	397 <token name="@UMI_GROUPING_HELP@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	398 UMI grouping options
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	399 --------------------
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	400
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	401 Grouping Method
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	402 ...............
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	403
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	404 What method to use to identify group of reads with the same (or
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	405 similar) UMI(s)?
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	406
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	407 All methods start by identifying the reads with the same mapping position.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	408
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	409 The simplest methods, unique and percentile, group reads with
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	410 the exact same UMI. The network-based methods, cluster, adjacency and
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	411 directional, build networks where nodes are UMIs and edges connect UMIs
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	412 with an edit distance <= threshold (usually 1). The groups of reads
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	413 are then defined from the network in a method-specific manner. For all
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	414 the network-based methods, each read group is equivalent to one read
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	415 count for the gene.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	416
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	417 - unique
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	418 Reads group share the exact same UMI
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	419
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	420 - percentile
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	421 Reads group share the exact same UMI. UMIs with counts < 1% of the
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	422 median counts for UMIs at the same position are ignored.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	423
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	424 - cluster
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	425 Identify clusters of connected UMIs (based on hamming distance
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	426 threshold). Each network is a read group
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	427
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	428 - adjacency
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	429 Cluster UMIs as above. For each cluster, select the node (UMI)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	430 with the highest counts. Visit all nodes one edge away. If all
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	431 nodes have been visited, stop. Otherwise, repeat with remaining
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	432 nodes until all nodes have been visted. Each step
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	433 defines a read group.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	434
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	435 - directional (default)
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	436 Identify clusters of connected UMIs (based on hamming distance
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	437 threshold) and umi A counts >= (2* umi B counts) - 1. Each
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	438 network is a read group.
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	439
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	440 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	441
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	442 <xml name="sambam_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	443 <section name="sambam" title="SAM/BAM options">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	444 <param argument="--mapping-quality" type="integer" value="0" label="Minimum mapping quality for a read to be retained"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	445 <param argument="--unmapped-reads" type="select" label="How to handle unmapped reads">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	446 <option value="discard">discard</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	447 <option value="use">use</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	448 <option value="correct">correct</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	449 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	450 <param argument="--chimeric-pairs" type="select" optional="true" label="How to handle chimeric read pairs (default: use)">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	451 <option value="discard">discard</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	452 <option value="use">use</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	453 <option value="correct">correct</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	454 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	455 <param argument="--unpaired-reads" type="select" optional="true" label="How to handle unpaired reads (default: use)">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	456 <option value="discard">discard</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	457 <option value="use">use</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	458 <option value="correct">correct</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	459 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	460 <param argument="--ignore-umi" type="boolean" truevalue="--ignore-umi" falsevalue="" label="Ignore UMI and dedup only on position"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	461 <param argument="--ignore-tlen" type="boolean" truevalue="--ignore-tlen" falsevalue="" label="Dedup paired end reads based solely on read1" help="whether or not the template length is the same"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	462 <param argument="--chrom" type="text" value="" label="Consider only chromosome" help="If a value is given only a single chromosome with the given name is considered"/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	463 <param argument="--subset" type="float" min="0.0" max="1.0" value="1.0" label="Only consider a random selection of the reads" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	464 <!--in-sam is set automatically-->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	465 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" label="BAM is paired end" help="This will also force the use of the template length to determine reads with the same mapping coordinates" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	466 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	467 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	468 <token name="@SAMBAM_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	469 --mapping-quality $sambam.mapping_quality
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	470 --unmapped-reads $sambam.unmapped_reads
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	471 #if $sambam.chimeric_pairs
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	472 --chimeric-pairs $sambam.chimeric_pairs
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	473 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	474 #if $sambam.unpaired_reads
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	475 --unpaired-reads $sambam.unpaired_reads
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	476 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	477 $sambam.ignore_umi
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	478 $sambam.ignore_tlen
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	479 #if str($sambam.chrom) != ''
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	480 --chrom '$sambam.chrom'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	481 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	482 --subset $sambam.subset
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	483 $sambam.paired
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	484 @SET_INPUT_TYPE@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	485 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	486
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	487 <!-- per-gene is hard coded in count https://github.com/CGATOxford/UMI-tools/blob/c3ead0792ad590822ca72239ef01b8e559802da9/umi_tools/count.py#L92
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	488 hence we need a specialized macro here
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	489 TODO count used XF as default for gene-tag now I set it explicitly for the tests but we could as well parametrize the macro and set tool specific defaults
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	490 -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	491
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	492 <xml name="fullsc_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	493 <expand macro="sc_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	494 <param argument="--per-gene" type="boolean" truevalue="--per-gene" falsevalue="" label="Deduplicate per gene"
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	495 help="Must combine with either --gene-tag or --per-contig. As for --per-contig except with this option you can align to a reference transcriptome with more than one transcript per gene. You need to also provide a map of genes to transcripts. This will also add a metacontig ('MC') tag to the output BAM file" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	496 </expand>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	497 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	498 <token name="@FULLSC_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	499 $sc.per_gene
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	500 @SC_OPTIONS@
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	501 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	502
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	503 <xml name="sc_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	504 <section name="sc" title="Single-cell RNA-Seq options">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	505 <yield/>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	506 <param argument="--gene-tag" type="text" optional="true" label="Deduplicate by this gene tag" help="As --per-gene except here the gene information is encoded in the bam read tag specified so you do not need to supply the mapping file">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	507 <expand macro="sanitize_tag" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	508 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	509 <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	510 <expand macro="sanitize_tag" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	511 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	512 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	513 <expand macro="barcode_sanitizer" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	514 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	515 <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	516 <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	517 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	518 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	519 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	520 <token name="@SC_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	521 #if str($sc.gene_tag) != "":
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	522 --gene-tag '$sc.gene_tag'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	523 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	524 #if str($sc.assigned_status_tag) != "":
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	525 --assigned-status-tag '$sc.assigned_status_tag'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	526 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	527 #if str($sc.skip_tags_regex) != "":
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	528 --skip-tags-regex '$sc.skip_tags_regex'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	529 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	530 $sc.per_contig
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	531 #if $sc.gene_transcript_map:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	532 --gene-transcript-map '$sc.gene_transcript_map'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	533 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	534 $sc.per_cell
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	535 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	536
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	537 <xml name="groupdedup_options_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	538 <section name="gd" title="group/dedup specific options">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	539 <param argument="--buffer-whole-contig" type="boolean" truevalue="--buffer-whole-contig" falsevalue="" label="Read whole contig before outputting bundles" help="Guarantees that no reads are missed, but increases memory usage" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	540 <!-- TODO this option is hidden on the CLI. Should we expose it? -->
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	541 <param argument="--whole-contig" type="boolean" truevalue="--whole-contig" falsevalue="" label="Consider all alignments to a single contig together" help="This is useful if you have aligned to a transcriptome multi-fasta" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	542 <param argument="--multimapping-detection-method" type="select" optional="true" label="BAM Tag indicating multimapping " help="Some aligners identify multimapping using bam tags. Setting this option to NH, X0 or XT will use these tags when selecting the best read amongst reads with the same position and umi">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	543 <option value="NH">NH</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	544 <option value="X0">X0</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	545 <option value="XT">XT</option>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	546 </param>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	547 </section>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	548 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	549 <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	550 $gd.buffer_whole_contig
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	551 $gd.whole_contig
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	552 $gd.multimapping_detection_method
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	553 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	554
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	555 <xml name="log_input_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	556 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" help="Choose if you want to generate a text file containing logging information" />
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	557 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	558 <xml name="log_output_macro">
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	559 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	560 <filter>log</filter>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	561 </data>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	562 </xml>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	563 <token name="@LOG@"><![CDATA[
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	564 #if $log:
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	565 --log='$out_log'
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	566 #end if
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	567 --log2stderr
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	568 ]]></token>
e654095ab143 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" iuc parents: 5 diff changeset	569
0 8db56d2f8b72 planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5 iuc parents: diff changeset	570 </macros>

Mercurial > repos > iuc > umi_tools_count

annotate macros.xml @ 8:e654095ab143 draft