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comparison kma_map.xml @ 1:95ab864b281a draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit a3fc5e6a1731ed2a63aed6b4c3e858bf4d9beecd"
author iuc
date Sat, 27 Nov 2021 09:36:00 +0000
parents 2595c27071c2
children
comparison
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0:2595c27071c2 1:95ab864b281a
1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
9 <version_command>kma -v</version_command> 9 <version_command>kma -v</version_command>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 kma 12 kma
13 -t \${GALAXY_SLOTS:-1} 13 -t \${GALAXY_SLOTS:-1}
14 -t_db '${kma_index.fields.path}' 14 -t_db '${kma_index.fields.path}'
15 #if $single_paired.single_paired_selector == 'paired' 15 #if $single_paired.single_paired_selector == 'paired'
16 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}' 16 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
17 #elif $single_paired.single_paired_selector == "paired_collection": 17 #elif $single_paired.single_paired_selector == "paired_collection":
18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' 18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
19 #else: 19 #else:
24 -k '${settings.kmer_size}' 24 -k '${settings.kmer_size}'
25 #end if 25 #end if
26 #if str($settings.p_value) 26 #if str($settings.p_value)
27 -p '${settings.p_value}' 27 -p '${settings.p_value}'
28 #end if 28 #end if
29 $settings.exhaustive_mode
29 ${settings.decontaminate} 30 ${settings.decontaminate}
30 ${settings.dense} 31 ${settings.dense}
31 ${settings.ref_fsa} 32 ${settings.ref_fsa}
32 ${settings.matrix} 33 ${settings.matrix}
33 ${settings.all_best_mappings} 34 ${settings.all_best_mappings}
58 #end if 59 #end if
59 #if str($settings.gapextend) 60 #if str($settings.gapextend)
60 -gapextend '${settings.gapextend}' 61 -gapextend '${settings.gapextend}'
61 #end if 62 #end if
62 ${settings.force_end_to_end} 63 ${settings.force_end_to_end}
64 -per $settings.pairing_reward
63 ${settings.set_cge_penalties_and_rewards} 65 ${settings.set_cge_penalties_and_rewards}
64 #end if 66 #end if
65 -o output 67 -o output
66 68
67 #if str($settings.advanced) == "advanced" and $settings.matrix 69 #if str($settings.advanced) == "advanced" and $settings.matrix
68 && gunzip output.mat.gz 70 && gunzip output.mat.gz
69 #end if 71 #end if
70 && gunzip output.frag.gz 72 && gunzip output.frag.gz
71 ]]> 73 ]]>
72 </command> 74 </command>
73 <inputs> 75 <inputs>
76 <option value="paired_collection">Paired collection</option> 78 <option value="paired_collection">Paired collection</option>
77 <option value="paired">Paired-end data</option> 79 <option value="paired">Paired-end data</option>
78 <option selected="True" value="single">Single-end data</option> 80 <option selected="True" value="single">Single-end data</option>
79 </param> 81 </param>
80 <when value="paired_collection"> 82 <when value="paired_collection">
81 <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" /> 83 <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
82 </when> 84 </when>
83 <when value="paired"> 85 <when value="paired">
84 <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> 86 <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
85 <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> 87 <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
86 </when> 88 </when>
87 <when value="single"> 89 <when value="single">
88 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/> 90 <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
89 </when> 91 </when>
90 </conditional> 92 </conditional>
91 <param name="kma_index" type="select"> 93 <param argument="-t_db" name="kma_index" type="select">
92 <options from_data_table="kma_index"> 94 <options from_data_table="kma_index">
93 <validator type="no_options" message="No KMA index available" /> 95 <validator type="no_options" message="No KMA index available" />
94 </options> 96 </options>
95 </param> 97 </param>
96 <conditional name="settings"> 98 <conditional name="settings">
99 <option value="advanced">Yes, see full parameter list.</option> 101 <option value="advanced">Yes, see full parameter list.</option>
100 </param> 102 </param>
101 <when value="simple"> 103 <when value="simple">
102 </when> 104 </when>
103 <when value="advanced"> 105 <when value="advanced">
104 <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" /> 106 <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
105 <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/> 107 <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
106 <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" /> 108 <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
107 <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" /> 109 <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
108 <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" /> 110 <param argument="-dense" name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
109 <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" /> 111 <param argument="-ref_fsa" name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
110 <param name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" /> 112 <param argument="-matrix" name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />
111 <param name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" /> 113 <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
112 <param name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" /> 114 <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
113 <param name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" /> 115 <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
114 <param name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" /> 116 <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
115 <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/> 117 <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
116 <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" /> 118 <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
117 <param name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" /> 119 <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />
118 <param name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" /> 120 <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />
119 <param name="reward" type="integer" min="1" value="1" max="100" label="Score for match" /> 121 <param argument="-reward" name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />
120 <param name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" /> 122 <param argument="-penalty" name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />
121 <param name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" /> 123 <param argument="-gapopen " name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />
122 <param name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" /> 124 <param argument="-gapextend" name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />
123 <param name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" /> 125 <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />
124 <param name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" /> 126 <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
125 </when> 127 </when>
126 </conditional> 128 </conditional>
127 </inputs> 129 </inputs>
128 <outputs> 130 <outputs>
129 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" /> 131 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />