Mercurial > repos > iuc > ncbi_fcs_gx

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit a23e39116e96db7282fa796a10e131bb2d91218b
author iuc
date Wed, 24 Sep 2025 13:29:42 +0000
parents a929a1a4ed97
children
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514b46297a38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit b1797a2dee3977cdf40d3cf413ab9ec1e0cb3f26
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1 <tool id="ncbi_fcs_gx" name="NCBI FCS GX" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>detects contamination from foreign organisms in genome sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $mode.mode_selector == "screen"
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10 #set manifest_pathname = $mode.config_tag.fields.local_manifest
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11 #if $mode.config_tag.fields.use_source_manifest == "1"
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12 #set manifest_pathname = $mode.config_tag.fields.source_manifest
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13 #end if
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14 GX_DB_DIR="\${TMPDIR}/$mode.config_tag" &&
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15 ## skip checksumming the database if the db_state_file exists
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16 if [ ! -e "\${GX_DB_DIR}/sync-files-completed.txt" ]; then
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17 ## copy data to local storage
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18 mkdir -p "\${GX_DB_DIR}" &&
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19 sync_files.py get --mft '$manifest_pathname' --dir "\${GX_DB_DIR}" > sync_files.log 2>&1 ||
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20 { cat sync_files.log >&2 ; false ; } &&
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21 touch "\${GX_DB_DIR}/sync-files-completed.txt";
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22 fi &&
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23 ## run gx
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24 GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py
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25 #if $mode.config_tag.fields.phone_home == "1"
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26 --phone-home-label '$mode.config_tag.fields.phone_home_label'
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27 #end if
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28 --fasta '$mode.fasta'
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29 #if $mode.id.id_selector == "gx_div"
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30 --tax-id '1'
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31 --div '$mode.id.div'
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32 #else
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33 --tax-id '$mode.id.tax_id'
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34 #end if
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35 #if $mode.species != ""
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36 --species '$mode.species'
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37 #end if
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38 --split-fasta '$mode.screen_adv.split_fasta'
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39 #if $mode.screen_adv.div
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40 --div '$mode.screen_adv.div'
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41 #end if
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42 #if $mode.screen_adv.ignore_same_kingdom
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43 --ignore-same-kingdom
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44 #end if
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45 --gx-db "\${GX_DB_DIR}"
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46 --out-basename output
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47 --action-report true
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48 --generate-logfile false
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49 #elif $mode.mode_selector == "clean"
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50 ## run gx
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51 GX_NUM_CORES=\${GALAXY_SLOTS:-2} gx clean-genome
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52 --input '$mode.input'
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53 --action-report '$mode.action_report'
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54 --contam-fasta-out 'contam.fa'
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55 --min-seq-len '$mode.min_seq_len'
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56 --output 'clean.fa'
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57 #end if
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58 ]]></command>
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59 <environment_variables>
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60 <environment_variable name="GX_ALIGN_EXCLUDE_TAXA">$getVar('mode.screen_adv.gx_align_exclude_taxa', '')</environment_variable>
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61 <environment_variable name="GX_EXTRA_CONTAM_DIVS"><![CDATA[#echo ','.join($getVar('mode.screen_adv.gx_extra_contam_divs', []))]]></environment_variable>
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62 </environment_variables>
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63 <inputs>
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64 <conditional name="mode">
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65 <param name="mode_selector" type="select" label="Choose the mode">
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66 <option value="screen" selected="true">Screen genome</option>
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67 <option value="clean">Clean genome</option>
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68 </param>
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69 <when value="screen">
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70 <!-- value, description, source_manifest, use_source_manifest, phone_home, phone_home_label, local_manifest -->
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71 <param name="config_tag" type="select" label="Database">
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72 <options from_data_table="ncbi_fcs_gx_databases_ext">
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73 <filter type="sort_by" column="1"/>
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74 </options>
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75 <validator message="No database is available" type="no_options"/>
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76 </param>
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77 <param argument="--fasta" type="data" format="fasta" label="Input file (Fasta file)" help="To detect contamination from foreign organisms, a genome assembly in a fasta file."/>
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78 <conditional name="id">
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79 <param name="id_selector" type="select" label="Taxonomy entry">
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80 <option value="gx_div" selected="true">GX Division</option>
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81 <option value="ncbi_tax">NCBI Taxonomic identifier</option>
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82 </param>
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83 <when value="gx_div">
2
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84 <!-- value, tag, description -->
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85 <param argument="--div" type="select" optional="true">
0
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86 <options from_data_table="ncbi_fcs_gx_divisions">
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87 <filter type="param_value" ref="config_tag" column="1" />
2
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88 <filter type="sort_by" column="2" />
0
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89 </options>
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90 <validator message="No GX Divisions are available" type="no_options"/>
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91 </param>
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92 </when>
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93 <when value="ncbi_tax">
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94 <!-- https://www.ncbi.nlm.nih.gov/taxonomy -->
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95 <param argument="--tax-id" type="text" label="Taxonomic identifier" help="The appropriate tax-id for your genome assembly. The appropriate tax-id for an organism can be retrieved from the NCBI Taxonomy website."/>
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96 </when>
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97 </conditional>
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98 <param argument="--species" type="text" optional="true" label="Species binomial name"/>
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99 <section name="screen_adv" title="Advanced options">
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100 <!-- comma separated list of taxa to ignore in GX_ALIGN_EXCLUDE_TAXA environment variable -->
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101 <param name="gx_align_exclude_taxa" type="text" value="" optional="true" label="Taxonomic identifier(s) to exclude" help="Multiple tax-ids may be provided as a comma-separated list.">
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102 <validator type="regex" message="comma separated integers">^\s*\d+\s*(,\s*\d+\s*)*$</validator>
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103 <sanitizer invalid_char="">
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104 <valid initial="string.digits">
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105 <add value=","/>
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106 </valid>
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107 </sanitizer>
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108 </param>
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109 <!-- value, tag, description -->
0
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110 <param name="gx_extra_contam_divs" type="select" multiple="true" optional="true" label="Additional contaminants to identify" help="Multiple gx-divisions may be selected.">
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111 <options from_data_table="ncbi_fcs_gx_divisions">
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112 <filter type="param_value" ref="config_tag" column="1" />
2
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113 <filter type="sort_by" column="2" />
0
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114 </options>
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115 <validator message="No GX Divisions are available" type="no_options"/>
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116 </param>
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117 <param argument="--split-fasta" type="boolean" checked="true" optional="true" label="Split fasta sequences on N-runs of length at least 10"/>
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118 <param argument="--div" type="text" value="" optional="true" label="BLAST-div of the tax-id" help="from 'NCBI BLAST name' on taxon Info page"/>
4
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119 <param argument="--ignore-same-kingdom" type="boolean" checked="false" optional="true" label="Ignore same-kingdom contamination"/>
0
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120 </section>
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121 </when>
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122 <when value="clean">
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123 <param argument="--input" type="data" format="fasta" label="Input file (Fasta file)" help="To detect contamination from foreign organisms, a genome assembly in a fasta file."/>
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124 <param argument="--action-report" type="data" format="tabular" label="Select Action report"/>
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125 <param argument="--min-seq-len" type="integer" value="200" label="Minimumm sequence length to keep"/>
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126 </when>
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127 </conditional>
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128 </inputs>
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129 <outputs>
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130 <!-- mode == screen -->
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131 <data name="taxonomy_report" format="tabular" from_work_dir="output.taxonomy.rpt" label="${tool.name} on ${on_string}: Taxonomy report">
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132 <filter>mode['mode_selector'] == 'screen'</filter>
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133 </data>
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134 <data name="action_report" format="tabular" from_work_dir="output.fcs_gx_report.txt" label="${tool.name} on ${on_string}: Action report">
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135 <filter>mode['mode_selector'] == 'screen'</filter>
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136 </data>
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137 <!-- mode == clean -->
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138 <data name="contam_fasta" format="fasta" from_work_dir="contam.fa" label="${tool.name} on ${on_string}: Fasta for EXCLUDE entries">
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139 <filter>mode['mode_selector'] == 'clean'</filter>
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140 </data>
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141 <data name="clean_fasta" format="fasta" from_work_dir="clean.fa" metadata_source="mode.input" label="${tool.name} on ${on_string}: Cleaned Fasta">
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142 <filter>mode['mode_selector'] == 'clean'</filter>
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143 </data>
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144 </outputs>
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145 <tests>
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146 <test expect_num_outputs="2">
6
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147 <conditional name="mode">
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148 <param name="mode_selector" value="screen"/>
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149 <param name="config_tag" value="test" />
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150 <param name="fasta" value="fcsgx_test.fa.gz" ftype="fasta"/>
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151 <conditional name="id">
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152 <param name="id_selector" value="ncbi_tax"/>
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153 <param name="tax_id" value="6973"/>
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154 </conditional>
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155 <section name="screen_adv"/>
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156 </conditional>
0
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157 <output name="taxonomy_report" file="output.taxonomy.rpt" compare="diff" lines_diff="2" />
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158 <output name="action_report" file="output.fcs_gx_report.txt" compare="diff" lines_diff="2" />
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159 </test>
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160 <test expect_num_outputs="2">
6
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161 <conditional name="mode">
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162 <param name="mode_selector" value="clean"/>
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163 <param name="input" value="fcsgx_test.fa.gz" ftype="fasta"/>
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164 <param name="action_report" value="output.fcs_gx_report.txt" ftype="tabular"/>
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165 </conditional>
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166 <output name="contam_fasta" decompress="true" file="output.contam.fa.gz" ftype="fasta" />
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167 <output name="clean_fasta" decompress="true" file="output.clean.fa.gz" ftype="fasta" />
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168 </test>
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169 </tests>
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170 <help><![CDATA[
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171 FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). The FCS-GX executable retrieves a Docker or Singularity container and runs a pipeline to align sequences to a large database of NCBI genomes through modified k-mer seeds and assign a most likely taxonomic division.
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172
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173 FCS-GX classifies sequences as contaminant when their taxonomic assignment is different from the user provided taxonomic identifier. A contamination summary provides an overview of observed contaminant divisions, counts, and total sizes, and an action report provides details and recommended actions for each problematic sequence.
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174
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175 https://github.com/ncbi/fcs/wiki/FCS-GX
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176 ]]></help>
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177 <expand macro="citations"/>
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178 </tool>