Mercurial > repos > lain > ms_to_peakforest_it

annotate ms2pf_it.xml @ 0:b58b229c4cbf draft

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author lain
date Fri, 03 Mar 2023 14:10:24 +0000
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1 <tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>
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3 adds you MS spectrum to peakforest.
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4 </description>
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5 <macros>
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <requirements>
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10 <requirement type="package" version="3.10">python</requirement>
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11 <requirement type="package">pyyaml</requirement>
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12 </requirements>
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13 <entry_points>
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14 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
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15 <port>8000</port>
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16 <url>/</url>
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17 </entry_point>
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18 </entry_points>
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19 <version_command>
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20 <![CDATA[
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21 python3 '$__tool_directory__/server.py' --version | head -n 1
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22 ]]>
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23 </version_command>
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24 <command>
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25 @MS2PF_COMMON_CMD@
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26 </command>
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27 <inputs>
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28 <expand macro="ms2pf_inputs" />
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29 </inputs>
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30 <outputs>
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31 <data name="ms2pfout" format="txt"
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32 label="${tool.name} on ${','.join(i.name for i in $input)}"
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33 />
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34 <data name="json_output" format="json"
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35 label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
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36 >
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37 <filter>do_output_json</filter>
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38 </data>
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39 </outputs>
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40 <tests>
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41 </tests>
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42 <help>
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43 <![CDATA[
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44 .. class:: infomark
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45
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46 **Authors** Lain Pavot (lain.pavot@inrae.fr)
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47
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48 .. class:: infomark
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49
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50 ---------------------------------------------------
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51
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52 ==============
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53 MS2 validation
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54 ==============
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55
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56 -----------
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57 Description
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58 -----------
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59
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60
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61 -----------------
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62 Workflow position
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63 -----------------
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64
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65 --------------
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66 Upstream tools
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67 --------------
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68
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69 +-------------------------+-----------------+--------+------------+
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70 | Name | output file | format | parameter |
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71 +=========================+=================+========+============+
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72 | ms2snoop | tsv | TSV | NA |
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73 +-------------------------+-----------------+--------+------------+
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74 | abinitfragnot | tsv | TSV | NA |
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75 +-------------------------+-----------------+--------+------------+
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76
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77 ----------------
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78 Downstream tools
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79 ----------------
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80
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81 +-------------------------+-----------------+--------+------------+
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82 | Name | output file | format | parameter |
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83 +=========================+=================+========+============+
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84 | NA | NA | NA | NA |
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85 +-------------------------+-----------------+--------+------------+
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86
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87
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88 -----------
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89 Input files
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90 -----------
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91
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92 +----------------------------------------------+------------+
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93 | Parameter : num + label | Format |
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94 +===========================+==================+============+
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95 | Output from ms2snoop or fragnot | TSV,CSV |
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96 +----------------------------------------------+------------+
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97
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98 ----------
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99 Parameters
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100 ----------
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101
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102 input
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103 | The file to process. Should contain spectra with mz, intensities and
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104 annotations
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105
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106 method
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107 | The method parameter tells which method was used. The value will
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108 be the default value in the peakforest form.
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109
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110 peakforest-url
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111 | The peakforest-url parameter tells which instance of peakforest to
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112 interact with
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113
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114 scan_type
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115 | The scan_type parameter which kind of scan was used. The value will
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116 be the default value in the peakforest form.
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117
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118 polarity
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119 | The polarity parameter which polarity was used. The value will
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120 be the default value in the peakforest form.
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121
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122 name
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123 | The name parameter provides names each spectra.
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124
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125
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126 ------------
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127 Output files
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128 ------------
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129
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130 There is not output file. When you run this tool, keep waiting until the
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131 « click here to display » link appears.
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132
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133 Click on the link to display peakforest form.
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134
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135 --------------
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136 Changelog/News
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137 --------------
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138
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139 1.0.0
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140 | First version, published on the toolshed.
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141
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142 ]]>
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143 </help>
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144 </tool>