Mercurial > repos > iuc > kma
comparison kma_map.xml @ 1:95ab864b281a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit a3fc5e6a1731ed2a63aed6b4c3e858bf4d9beecd"
author | iuc |
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date | Sat, 27 Nov 2021 09:36:00 +0000 |
parents | 2595c27071c2 |
children | 98099e4da1fd |
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0:2595c27071c2 | 1:95ab864b281a |
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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" /> |